Quran 8:12-13 - I will instill terror into the hearts of the unbelievers

8:12-13... I will instill terror into the hearts of the unbelievers. Smite ye above their necks and smite all their finger tips off them. This because they contend against God and his apostle. ...

This is another ayah that is commonly quoted out of context, both historical context and the context of the ayah itself in the Qur'an. Let us first examine the full ayah: 

إِذْ يُوحِي رَ‌بُّكَ إِلَى الْمَلَائِكَةِ أَنِّي مَعَكُمْ فَثَبِّتُوا الَّذِينَ آمَنُوا ۚ سَأُلْقِي فِي قُلُوبِ الَّذِينَ كَفَرُ‌وا الرُّ‌عْبَ فَاضْرِ‌بُوا فَوْقَ الْأَعْنَاقِ وَاضْرِ‌بُوا مِنْهُمْ كُلَّ بَنَانٍ ﴿١٢﴾ ذَٰلِكَ بِأَنَّهُمْ شَاقُّوا اللَّـهَ وَرَ‌سُولَهُ ۚ وَمَن يُشَاقِقِ اللَّـهَ وَرَ‌سُولَهُ فَإِنَّ اللَّـهَ شَدِيدُ الْعِقَابِ ﴿١٣﴾

8:12-13 Recall that your Lord inspired the angels: "I am with you; so support those who believed. I will throw terror into the hearts of those who disbelieved. You may strike them above the necks, and you may strike even every finger." This is what they have justly incurred by FIGHTING God and His messenger. For those who fight against God and His messenger, God's retribution is severe.

That is the context of the ayah in the Qur'an. The historical context is that this verse was revealed at the Battle of Badr, a battle in which the pagans of Makkah traveled over 200 miles to destroy the Muslims of Madinah. The Pagans of Makkah had an army of about 1000 while the Muslims were only 300 followers. The Prophet Muhammad ((peace be upon him)) and his followers had suffered severe persecutions and torture for 13 years in the city of Makkah. Having fled from Makkah to the safety of Madinah, they found that they were once again threatened. Abul 'Ala Maududi describes the situation that led to the Battle of Badr, beginning with the Muslim activity in Madinah:

In the first year of Hijrah, four expeditions were sent [by the Muslims to the Quraish], that is, the expedition under Hamzah, the expedition under Ubaidah bin Harith, the expedition under Sa'ad bin Abi Waqqas and the Al-Abwa' expedition under the Holy Prophet himself. In the first month of the second year two more incursions were made on the same route. These are known as Buwat Expedition and Zawal Ushairah Expedition. Two things about all these expeditions are noteworthy. First, no blood was shed and no caravans were plundered in any of these expeditions. This proves that the real object of these expeditions was to show to the Quraish which way the wind was blowing. Secondly, not a single man from the people of Al-Madinah was sent by the Holy. Prophet on any of these incursions. All the bands consisted purely of the immigrants from Makkah so that the conflict should remain between the people of the Quraish themselves and should not further spread by the involvement of other clans. On the other side, the Quraish of Makkah tried to involve others also in the conflict. When they sent bands towards Al-Madinah, they did not hesitate to plunder the people. For instance, an expedition under the leadership of Kurz bin Jabir al-Fihrl plundered the cattle of the people of Al-Madinah from the very vicinity of the city to show what their real intentions were. This was the state of affairs when, in Sha'aban, 2 A. H. (February or March, 623 A. D.) a big trade caravan of the Quraish, carrying goods worth $50,000 or so, with only a guard of thirty to forty men, on its way back from Syria to Makkah, reached the territory from where it could be easily attacked from Al-Madinah. As the caravan was carrying trade goods worth thousands of pounds, and was scantily guarded, naturally Abu Sufyan, who was in charge of it, from his Past experience feared an attack from the Muslims. Accordingly, as soon as he entered the dangerous territory, he despatched a camel rider to Makkah with a frantic appeal for help. When the rider reached Makkah, he, following an old custom of Arabia, tore open the ears of his camel, cut open his nose and overturned the saddle. Then rending his shirt from front and behind, he began to cry aloud at the top of his voice, "O people of Quraish despatch help to protect your caravan from Syria under the charge of Abu Sufyan, for Muhammad with his followers is in pursuit of it; otherwise I don't think you will ever get your goods. Run, run for help." This caused great excitement and anger in the whole of Makkah and all the big chiefs of the Quraish got ready for war. An army, consisting of 600 armored soldiers and cavalry of 100 riders with great pomp and show marched out for a fight. They intended not only to rescue the caravan but also to put to an end, once for all, the new menace from the Muslims who had consolidated themselves at Al-Madinah. They wanted to crush that rising power and overawe the clans surrounding the route so as to make it absolutely secure for future trade... ...the Holy Prophet and the true Believers had realized the urgency of that critical hour which required the risk of life: therefore they marched straight to the south-west, wherefrom the army of the Quraish was coming. This is a clear proof of the fact that from the very beginning they had gone out to fight with the army and not to plunder the caravan. For if they had aimed at plundering the caravan they would have taken the north- westerly direction and not the south- westerly one. (Maududi, Tafheem Al-Qur'an, emphasis added)

The Makkans were not satisfied with expelling the Muslims from Makkah and subsequently desired that they be purged from the surroundings of all major trade routes. So God supported the Muslims and informed them that God would allow justice to prevail over oppression. He informed them that they should not fear fighting in God's path, but it is the enemies who should fear God's retribution for their oppression and injustice. Also, God inspired the ANGELS to support the believers and strike the disbelievers. This was NOT a command for the Muslims. Shaykh Safiur Rahman Al-Mubarakpuri describes the situation during the Battle of Badr as follows:

[The Makkans] were too much exasperated and enraged and fell upon the Muslims to exterminate them once and for all. The Muslims, however, after supplicating their Lord, calling upon Him for assistance, were made to hold to their position and conduct a defensive war plan that was successful enough to inflict heavy losses on the attackers. The Prophet (Peace be upon him) used to pray to his Lord ceaselessly persistently and day and night to come to their succour. When the fierce engagement grew too hot he again began to supplicate his Lord saying: “O Allâh! Should this group (of Muslims) be defeated today, You will no longer be worshipped.”.... Immediate was the response from Allâh, Who sent down angels from the heavens for the help and assistance of the Prophet (Peace be upon him) and his companions. The Noble Qur’ân observes: And recall when your Lord inspired the angels: “Verily, I am with you, so keep firm those who have believed. I will cast terror into the hearts of those who have disbelieved.” [8:12]
(Al-Mubarakpuri, Ar-Raheeq Al-Makhtum; Riyadh-Saudi Arabia, Dar-us-Salam Publications, 1996; pp. 219-220)

Also, the previously mentioned laws of Jihad all applied here and the Muslims were commanded:

8:61 But if the enemy incline towards peace, do thou (also) incline towards peace, and trust in God: for He is One that hears and knows (all things).

وَإِن جَنَحُوا لِلسَّلْمِ فَاجْنَحْ لَهَا وَتَوَكَّلْ عَلَى اللَّـهِ ۚ إِنَّهُ هُوَ السَّمِيعُ الْعَلِيمُ ﴿٦١﴾

Believing in a punishment for oppressive disbelievers delivered by the unseen angels is hardly different from believing in an unseen punishment in the next life.

Quran (5:54) & (48:29): "Ruthless to the disbelievers..."

5:54 Allah will bring a people whom He loveth and who love Him, humble toward believers, stern toward disbelievers, striving in the way of Allah, and fearing not the blame of any blamer. Such is the grace of Allah which He giveth unto whom He will. Allah is All-Embracing, All-Knowing. 48:29 Mohammed is Allah's apostle. Those who follow him are ruthless to the unbelievers but merciful to one another

Non-Muslims think that this verse tells Muslims to be harsh and cruel to non-Muslims. Let us first provide a better translation: 

مُّحَمَّدٌ رَّ‌سُولُ اللَّـهِ ۚ وَالَّذِينَ مَعَهُ أَشِدَّاءُ عَلَى الْكُفَّارِ‌ رُ‌حَمَاءُ بَيْنَهُمْ ۖ تَرَ‌اهُمْ رُ‌كَّعًا سُجَّدًا يَبْتَغُونَ فَضْلًا مِّنَ اللَّـهِ وَرِ‌ضْوَانًا ۖ سِيمَاهُمْ فِي وُجُوهِهِم مِّنْ أَثَرِ‌ السُّجُودِ ۚ ذَٰلِكَ مَثَلُهُمْ فِي التَّوْرَ‌اةِ ۚ وَمَثَلُهُمْ فِي الْإِنجِيلِ كَزَرْ‌عٍ أَخْرَ‌جَ شَطْأَهُ فَآزَرَ‌هُ فَاسْتَغْلَظَ فَاسْتَوَىٰ عَلَىٰ سُوقِهِ يُعْجِبُ الزُّرَّ‌اعَ لِيَغِيظَ بِهِمُ الْكُفَّارَ‌ ۗ وَعَدَ اللَّـهُ الَّذِينَ آمَنُوا وَعَمِلُوا الصَّالِحَاتِ مِنْهُم مَّغْفِرَ‌ةً وَأَجْرً‌ا عَظِيمًا ﴿٢٩﴾

48:29 Muhammad is the apostle of Allah. and those who are with him are strong against disbelievers, (but) compassionate amongst each other. Thou wilt see them bow and prostrate themselves (in prayer), seeking Grace from Allah and (His) Good Pleasure. On their faces are their marks, (being) the traces of their prostration. This is their similitude in the Taurat; and their similitude in the Gospel is: like a seed which sends forth its blade, then makes it strong; it then becomes thick, and it stands on its own stem, (filling) the sowers with wonder and delight. As a result, it fills the Unbelievers with rage at them. Allah has promised those among them who believe and do righteous deeds forgiveness, and a great Reward.

The Arabic word "ashidda" does not mean ruthless, but strong and firm. Ruthless is an unacceptable translation. Translations of ashidda:

Pickthall: hard; Yusuf Ali: strong; Daryabadi: stern; Khan-Hilali: severe; F. Malik: strong; Shakir: firm of heart; Arberry: hard; Irving: strict

Also, the disbelievers being referred to in these verses are the those who persecuted and attacked the Muslims. Shaykh Fawzee Al-Atharee said the following:

And similarly the disbeliever, if he has good character with us and good manners with us and good way and treatment with us, then we have good manners with him, good behaviour with him, good way with him and good treatment of him. And if his manners are bad and his behaviour is bad [i.e. abusive and cruel], then we treat him with accordance to how he is treating us. This is something permissible in the legislation. But the Prophet s.a.w.s. has indicated very clearly in all the narrations that have been brought and throughout his life, that there must be a matter of balance and to be just. And that is in dealing with the people of disbelief and also in dealing with those who have faith.

The Muslims were commanded to stand up for their religion and defend themselves against the persecution of the disbelievers. Again, if we examine the historical context, we also find that this is referring to those who attacked the Muslims continuously. So verses apply in a situation similar to the historical context. Since this verse mentions the companions of the Prophet Muhammad (peace be upon him) and praises their path, let us examine some narrations about the companions. Musab bin Umair was a notable companion of the Prophet Muhammad (peace be upon him). He was sent to Madinah to share the message of Islam with the people living there. One incident of his related as follows:

Once Musab and Sad were sitting near a well in an orchard of the Zafar clan. With them were a number of new Muslims and others who were interested in Islam. A powerful notable of the city, Usayd ibn Khudayr, came up brandishing a spear. He was livid with rage. Sad ibn Zararah saw him and told Musab: "This is a chieftain of his people. May God place truth in his heart." "If he sits down, I will speak to him," replied Musab, displaying all the calm and tact of a great daiy. The angry Usayd shouted abuse and threatened Musab and his host. "Why have you both come to us to corrupt the weak among us? Keep away from us if you want to stay alive." Musab smiled a warm and friendly smile and said to Usayd: "Won't you sit down and listen? If you are pleased and satisfied with our mission. accept it and if you dislike it we would stop telling you what you dislike and leave." "That's reasonable," said Usayd and, sticking his spear in the ground, sat down. Musab was not compelling him to do anything. He was not denouncing him. He was merely inviting him to listen. If he was satisfied, well and good. If not, then Musab would leave his district and his clan without any fuss and go to another district. Musab began telling him about Islam and recited the Quran to him. Even before Usayd spoke, it was clear from his face, now radiant and expectant, that faith had entered his heart. He said: "How beautiful are these words and how true! What does a person do if he wants to enter this religion?" "Have a bath, purify yourself and your clothes. Then utter the testimony of Truth (Shahadah), and perform Salat. Usayd left the gathering and was absent for only a short while. He returned and testified that there is no god but Allah and that Muhammad is the Messenger of Allah. (SOURCE)

Another example is found in the treatment of Thumamah Ibn Uthal, who was a notorious criminal who had killed many Muslim travelers. Because of this, the Prophet Muhammad declared him a wanted criminal who was to be captured or killed. Soon after, when he was traveling for pilgrimage, some Muslims caught him and took him to the Prophet Muhammad (peace be upon him). The Prophet recognized him and had him kept in the Masjid (mosque) with food and even ordered his own camel to be milked for him. They treated him like a guest rather than a war criminal! The Prophet Muhammad asked Thumamah what he had to say for himself, to which he replied "If you want to kill in reprisal, you can have someone of noble blood to kill. If, out of your bounty, you want to forgive, I shall be grateful. If you want money in compensation, I shall give you whatever amount you ask." The Prophet Muhammad freed him and allowed him to leave. The very same day, Thumamah returned and declared his acceptance of Islam to the Prophet Muhammad. So we find that the Prophet Muhammad (peace be upon him) and his companions displayed the best character and attitude towards all people and this is what drew so many people to Islam. As the God says in the Qur'an:

3:159. And by the Mercy of God, you dealt with them gently. And had you been severe and harsh-hearted, they would have ran away from about you; so pass over (their faults), and ask (God's) Forgiveness for them; and consult them in the affairs. Then when you have taken a decision, put your trust in All‚h, certainly, All‚h loves those who put their trust (in Him).

فَبِمَا رَ‌حْمَةٍ مِّنَ اللَّـهِ لِنتَ لَهُمْ ۖ وَلَوْ كُنتَ فَظًّا غَلِيظَ الْقَلْبِ لَانفَضُّوا مِنْ حَوْلِكَ ۖ فَاعْفُ عَنْهُمْ وَاسْتَغْفِرْ‌ لَهُمْ وَشَاوِرْ‌هُمْ فِي الْأَمْرِ‌ ۖ فَإِذَا عَزَمْتَ فَتَوَكَّلْ عَلَى اللَّـهِ ۚ إِنَّ اللَّـهَ يُحِبُّ الْمُتَوَكِّلِينَ ﴿١٥٩﴾

The Prophet Muhammad (peace be upon him) was commanded by God to bring people to the teachings of Islam through the beautiful character that Muslims must show. The Prophet Muhammad (peace be upon him) conveyed this message to others by saying:

He who is not merciful to others, will not be treated mercifully. (Muslim, Volume 8, Book 73, Number 42)

And there are numerous examples one could quote which illustrate the kind and loving nature of the Prophet Muhammad (peace be upon him).

Narrated Abu Huraira: A disbelieving Bedouin urinated in the mosque, and the people rushed to beat him. Allah's Apostle ordered them to leave him, let him finish and pour a bucket or a tumbler (full) of water over the place where he has passed urine. The Prophet then explained to the Bedouin calmly, "This is a place of worship, in it is the worship of God and the reading of Qur'an." After the Bedouin had left, the Prophet then said to his companions, " You have been sent to make things easy (for the people) and you have not been sent to make things difficult for them." (Muslim, Book 2, Number 559 and Bukhari, Volume 8, Book 73, Number 149)

This narration, on its own, is sufficient to refute the claim that Islam is intolerant. The Prophet Muhammad (peace be upon him) did not show any anger or resentment to a non-Muslim who urinated in the Muslims place of worship! So Islam teaches gentleness in all things. As the Prophet Muhammad said:

Whoever is deprived of gentleness is deprived of all good. (Muslim, Book 32, Number 6270 & Abu Dawood, Book 41, Number 4791)

The Prophet Muhammad (peace be upon him) always displayed tolerance and compassion in his dealings with people, including Non-Muslims. Dr. M. Hamidullah explains the following points:

When the Prophet Mohammed settled down in Medina, he found there complete anarchy, the region having never known before either a State or a king to unite the tribes torn by internecine feuds. In just a few weeks, he succeeded in rallying all the inhabitants of the region into order. He constituted a city state, in which Muslims, Jews, pagan Arabs and also probably a small number of Christians, all entered into a statal organism by means of a social contract. The constitutional law of this first 'Muslim' State - which was the confederacy as a sequence of the multiplicity of the population groups - has come down to us in toto, and we read therein not only in clause 25: "to Muslims their religion, and to Jews their religion," or, "that there would be benevolence and justice," but even the unexpected passage in the same clause 25: "the Jews . . . are a community (in alliance) with - according Ibn Hisham and in the version of Abu-'Ubaid, a community (forming part) of - the believers (i.e., Muslims)." The very fact that, at the time of the constitution of this city-state, the autonomous Jewish villages acceded of their free will to the confederal State, and recognized Muhammad as their supreme political head, implies in our opinion that the non-Muslim subjects possessed the right of votes in the election of the head of the Muslim State, at least in so far as the political life of the country was concerned. (Hamidullah, Introduction to Islam, paragraphs 414-416)

During the life of Prophet Muhammad, there was a Jewish synagogue in Madinah and an educational institute known as Bait Al-Midras. The Prophet Muhammad (peace be upon him) preserved and protected both of them. The Prophet Muhammad (peace be upon him) also honored a group of Christians of najran from Yemen, when they visited his mosques in Madinah. The Prophet Muhammad (peace be upon him) held interfaith discussions with them and they prayed in the Mosque in the Christian fashion while the Muslims prayed in the Islamic tradition. The Prophet Muhammad's tolerance is also illustrated in the following narration:

Once the Prophet was seated at some place in Madinah, along with his Companions. During this time a funeral procession passed by. On seeing this, the Prophet stood up. One of his Companion remarked that the funeral was that of a Jew. The Prophet replied, “Was he not a human being?” (Bukhari, Muslim)

If every human being in this world saw the various ethnicities and cultures with these eyes, the world would flourish in peace and harmony. The Prophet Muhammad (peace be upon him) set an example for his companions to follow in the way he showed respect and kindness to Non-Muslims. Dr. Farida Khanam also points out the following incidents:

In the present world, everyone’s thinking, tastes, aptitude, likes and dislikes can never exactly coincide. For many reasons, differences do arise in this world. But then, what is the permanent solution to the problem? The solution lies in tolerance, called i‘raz in Arabic. The Prophet’s entire life served as a perfect example of this principle. According to his wife, ‘A’isha, "He was a personification of the Qur’an." That is to say, the Prophet molded his own life in accordance with the ideal pattern of life which he presented to others in the form of the Qur’an. He never beat a servant, or a woman, or anyone else. He did, of course, fight for what was right. Yet, when he had to choose between two alternatives, he would take the easier course, provided it involved no sin.’ No one was more careful to avoid sin than he. He never sought revenge—on his own behalf—for any wrong done to him personally. Only if God’s commandments had been broken would he mete out retribution for the sake of God. It was such conduct which gained the Prophet universal respect. In the early Meccan period when the antagonists far exceeded the Prophet’s companions in number, it often happened that when the Prophet would stand to pray, his detractors would come near him and whistle and clap in order to disturb him, but the Prophet did not even once show his anger at such acts. He always opted for the policy of tolerance and avoidance of confrontation... When the opposition became very strong the Prophet left Mecca for Medina. But his antagonists did not leave him in peace. They began to attack Medina. In this way a state of war prevailed between the Muslims and non-Muslims. Since the Prophet avoided war at all costs, he strove to bring about a peace agreement between him and the Meccans. After great efforts on his part, the non-Muslims agreed to the finalizing of a 10-year peace treaty, which was drafted and signed at the al-Hudaybiyyah. While the al-Hudaybiyyah treaty was being drafted, the Meccans indulged in a number of extremely provocative acts. For instance, the agreement mentioned the Prophet’s name as ‘Muhammad the Messenger of God.’ They insisted that the phrase ‘the messenger of God’ should be taken out, and be replaced simply by ‘Muhammad, son of Abdullah’. The Prophet accepted their unreasonable condition and deleted the appellation with his own hands. Similarly, they made the condition that if they could lay their hands on any Muslim they would make him a hostage, but if the Muslims succeeded in detaining any non-Muslim, they would have to set him free. The Prophet even relented on this point. For the restoration of peace in the region, the Prophet accepted a number of such unjustifiable clauses as were added by the enemy. In this way he set the example of peace and tolerance being linked with one another. If we desire peace, we must tolerate many unpleasant things from others. There is no other way to establish peace in society. (SOURCE)

The Prophet Muhammad (peace be upon him) also extended the hand of friendship to Christians as well. He maintained good ties with the Christian Negus of Abyssinia throughout his life. The Prophet Muhammad (peace be upon him) even selected Non-Muslims as ambassadors. One such example was Amr ibn Umaiyah Ad-Damri. The Prophet Muhammad (peace be upon him) sent a message to the Monks of Saint Catherine in Mount Sinai, saying the following: "

This is a message written by Muhammad ibn Abdullah, as a covenant to those who adopt Christianity, far and near, we are behind them. Verily, I defend them by myself, the servants, the helpers, and my followers, because Christians are my citizens; and by Allah! I hold out against anything that displeases them. No compulsion is to be on them. Neither are their judges to be changed from their jobs, nor their monks from their monasteries. No one is to destroy a house of their religion, to damage it, or to carry anything from it to the Muslims' houses. Should anyone take any of these, he would spoil God's covenant and disobey His Prophet. Verily, they (Christians) are my allies and have my secure charter against all that they hate. No one is to force them to travel or to oblige them to fight. The Muslims are to fight for them. If a female Christian is married to a Muslim, this is not to take place without her own wish. She is not to be prevented from going to her church to pray. Their churches are to be respected. They are neither to be prevented from repairing them nor the sacredness of their covenants. No one of the nation is to disobey this covenant till the Day of Judgment and the end of the world."

The Prophet Muhammad (peace be upon him) also advised his companion Mu'adh ibn Jabal by saying:

No Jew is to be annoyed because of their Judaic faith.

We must also examine the Prophet Muhammad's teachings towards neighbors:

Abu Huraira (May Allah be pleased with him) reported: The Prophet (peace be upon him) said, "By Allah, he is not a believer! By Allah, he is not a believer! By Allah, he is not a believer.'' It was asked, "Who is that, O Messenger of Allah?'' He said, "One whose neighbor does not feel safe from his evil". (Al-Bukhari and Muslim)
"He who believes in God and the Last Day should honour his guest, should not harm his neighbor, should speak good or keep quiet." (Bukhari, Muslim)

The Prophet Muhammad (peace be upon him) also clearly specified that a Non-Muslim neighbor should receive this excellent treatment:

"Whoever hurts a Non-Muslim citizen of a Muslim state hurts me, and he who hurts me annoys God." (Bukhari)
"He who hurts a Non-Muslim citizen of a Muslim state, I am his adversary, and I shall be his adversary on the Day of a Judgment." (Bukhari)

It is fascinating to note that the Prophet Muhammad (peace be upon him) was so vocal in his support of good treatment towards humanity that he would even be prepared to stand on the side of the Non-Muslims against the Muslims who did not follow his teachings. This is true justice and this is what lead to the peace and prosperity that Islam brought into the world. The excellent character of Prophet Muhammad (peace be upon him) has been noted by many Non-Muslim historians as well, and in fact anyone who has studied his life carefully has been amazed at the golden character of this human being. Washington Irving notes in his book 'Mahomet and His Successors':

In his private dealings he was just. He treated friends and strangers, the rich and poor, the powerful and weak, with equity, and was beloved by the common people for the affability with which he received them, and listened to their complaints. (Irving, Mahomet and His Successors)

Quran 9:5 Kill the disbelievers wherever you find them ?!

9:5 Kill the disbelievers wherever you find them.

This ayah has been misquoted . First, we shall provide the verse in its context: 

فَإِذَا انسَلَخَ الْأَشْهُرُ‌ الْحُرُ‌مُ فَاقْتُلُوا الْمُشْرِ‌كِينَ حَيْثُ وَجَدتُّمُوهُمْ وَخُذُوهُمْ وَاحْصُرُ‌وهُمْ وَاقْعُدُوا لَهُمْ كُلَّ مَرْ‌صَدٍ ۚ فَإِن تَابُوا وَأَقَامُوا الصَّلَاةَ وَآتَوُا الزَّكَاةَ فَخَلُّوا سَبِيلَهُمْ ۚ إِنَّ اللَّـهَ غَفُورٌ‌ رَّ‌حِيمٌ ﴿٥﴾ وَإِنْ أَحَدٌ مِّنَ الْمُشْرِ‌كِينَ اسْتَجَارَ‌كَ فَأَجِرْ‌هُ حَتَّىٰ يَسْمَعَ كَلَامَ اللَّـهِ ثُمَّ أَبْلِغْهُ مَأْمَنَهُ ۚ ذَٰلِكَ بِأَنَّهُمْ قَوْمٌ لَّا يَعْلَمُونَ ﴿٦﴾

9:5-6 But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for Allah is Oft-forgiving, Most Merciful. If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah. and then escort him to where he can be secure. That is because they are men without knowledge.

Having presented the verse in context, we can analyze it properly. Dr. Maher Hathout gives an explanation on the historical context of the verse:

This verse was revealed towards the end of the revelation period and relates to a limited context. Hostilities were frozen for a three-month period during which the Arabs pledged not to wage war. Prophet Muhammad was inspired to use this period to encourage the combatants to join the Muslim ranks or, if they chose, to leave the area that was under Muslims rule; however, if they were to resume hostilities, then the Muslims would fight back until victorious. One is inspired to note that even in this context of war, the verse concludes by emphasizing the divine attributes of mercy and forgiveness. To minimize hostilities, the Qur'an ordered Muslims to grant asylum to anyone, even an enemy, who sought refuge. Asylum would be granted according to the customs of chivalry; the person would be told the message of the Qur'an but not coerced into accepting that message. Thereafter, he or she would be escorted to safety regardless of his or her religion. (9:6). (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, pp.52-53, emphasis added)

Therefore, this verse once again refers to those pagans who would continue to fight after the period of peace. It clearly commands the Muslims to protect those who seek peace and are non-combatants. It is a specific verse with a specific ruling and can in no way be applied to general situations. The command of the verse was only to be applied in the event of a battle. As Abdullah Yusuf Ali writes:

The emphasis is on the first clause: it is only when the four months of grace are past, and the other party show no sign of desisting from their treacherous design by right conduct, that the state of war supervenes - between Faith and Unfaith. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary, emphasis added)

If the pagans would not cease their hostilities towards the Muslims, then they were to be fought, especially since they were living in the land of an Islamic state. Dr. Zakir Naik writes concerning this verse:

This verse is quoted during a battle. ...We know that America was once at war with Vietnam. Suppose the President of America or the General of the American Army told the American soldiers during the war: "Wherever you find the Vietnamese, kill them". Today if I say that the American President said, "Wherever you find Vietnamese, kill them" without giving the context, I will make him sound like a butcher. But if I quote him in context, that he said it during a war, it will sound very logical, as he was trying to boost the morale of the American soldiers during the war. ...Similarly in Surah Taubah chapter 9 verse 5 the Qur'an says, "Kill the Mushriqs (pagans) where ever you find them", during a battle to boost the morale of the Muslim soldiers. What the Qur'an is telling Muslim soldiers is, don't be afraid during battle; wherever you find the enemies kill them. Surah Taubah chapter 9 verse 6 gives the answer to the allegation that Islam promotes violence, brutality and bloodshed. It says: "If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge." [Al-Qur'an 9:6]
The Qur'an not only says that a Mushriq seeking asylum during the battle should be granted refuge, but also that he should be escorted to a secure place. In the present international scenario, even a kind, peace-loving army General, during a battle, may let the enemy soldiers go free, if they want peace. But which army General will ever tell his soldiers, that if the enemy soldiers want peace during a battle, don't just let them go free, but also escort them to a place of security? This is exactly what Allah (swt) says in the Glorious Qur'an to promote peace in the world. (SOURCE, emphasis added)

Dr. Naik makes some very interesting observations about the verse. Indeed, it is truly amazing how Islam-haters will ignore God's infinite mercy in their attempt to malign Islam. God has always given human beings a way out of any suffering, and has only ordained fighting as a last resort. Muslim scholars have written much commentary on these Qur'anic verses explaining the historical context in such great detail so that there may be no misconceptions. We have quoted extensively from various commentators on these verses and there is no need to repeat the same material again. We will provide one more commentary before moving on. Professor Shahul Hameed writes on verse 9:5:

This is a verse taken from Surah At-Tawba. This chapter of the Qur’an was revealed in the context when the newly organized Muslim society in Madinah was engaged in defending themselves against the pagan aggressors. The major question dealt with here is, as to how the Muslims should treat those who break an existing treaty at will. The first clause in the verse refers to the time-honored Arab custom of a period of warning and waiting given to the offenders, after a clear violation. That is, they will be given four months’ time to repair the damage done or make peace. But if nothing happens after the expiry of these forbidden months, what should be done? This is what the present verse says. According to this verse, fighting must be resumed until one of the two things happens: Either the enemy should be vanquished by relentless fighting. That is what is meant by {then fight and slay the pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem [of war]}; or they should repent, establish prayers and pay zakah, etc. This is one of those verses of the Qur’an which are likely to be misunderstood, if quoted out of context. We must understand that this fighting was against a people who forced the Prophet and his companions to leave not only their own homes but all their property and even their hometown of Makkah to Madinah. Once the Muslims were organized into a community in those lawless times, the rules to be followed by the Muslims were clearly laid down, even in the matter of war. Since Islam is a comprehensive system, no human activity could be ignored. And given the nature of mankind, we cannot imagine a situation where fighting is completely ruled out either. As can be seen, the above injunctions on fighting is not on an individual level, but only in the case of a society that strives to flourish and thrive as a nation. But even here the norms are clear: fighting is only in self defence or for the establishment of justice; and always fighting is the last option. And no one is allowed to transgress the limits set by God. (SOURCE, emphasis added)

Ibn al-`Arabi, in his commentary on the Qur’an, writes:

“It is clear from this that the meaning of this verse is to kill the pagans who are waging war against you.” (Ahkam al-Qur’an: 2/456, emphasis added)

Shaykh Sami al-Majid also makes some very interesting points in his discussion on this verse:

If we look at the verses in Sûrah al-Tawbah immediately before and after the one under discussion, the context of the verse becomes clear. A few verses before the one we are discussing, Allah says: “There is a declaration of immunity from Allah and His Messenger to those of the pagans with whom you have contracted mutual alliances. Go then, for four months, to and fro throughout the land. But know that you cannot frustrate Allah that Allah will cover with shame those who reject Him.” [Sûrah al-Tawbah: 1-2]
In these verses we see that the pagans were granted a four month amnesty with an indication that when the four months were over, fighting would resume. However, a following verse exempts some of them from the resumption of hostilities. It reads:
“Except for those pagans with whom you have entered into a covenant and who then do not break their covenant at all nor aided anyone against you. So fulfill your engagements with them until the end of their term, for Allah loves the righteous.” [Sûrah al-Tawbah: 4]
So when Allah says: “But when the forbidden months are past, then fight the pagans wherever you find them, and seize them and beleaguer them and lie in wait for them in every stratagem (of war)” we must know that it is not general, since the verse above has qualified it to refer to the pagan Arabs who were actually at war with the Prophet (peace be upon him) and those who broke their covenants of peace. This is further emphasized a few verses later where Allah says:
“Will you not fight people who broke their covenants and plotted to expel the Messenger and attacked you first?” [Sûrah al-Tawbah: 13] (SOURCE)

Therefore, the context of the verse within the Surah makes it clear that this refers to those who are persistent in their hostilities and attacks against Muslims, and it is applied in battle only. We recommend that one reads Shaykh Sami Al-Majid's full article entitled There is no Compulsion in Religion.

Quran 2:191 And slay them wherever ye catch them.

And slay them wherever ye catch them.." (2:191)

A classic and popular example of what Muslim scholars call a ‘cut and paste’ approach. Everything becomes so much easier for the Anti-Islamists when they remove the context. The solution is to simply replace the verse in its context:

وَقَاتِلُوا فِي سَبِيلِ اللَّـهِ الَّذِينَ يُقَاتِلُونَكُمْ وَلَا تَعْتَدُوا ۚ إِنَّ اللَّـهَ لَا يُحِبُّ الْمُعْتَدِينَ ﴿١٩٠﴾وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِ‌جُوهُم مِّنْ حَيْثُ أَخْرَ‌جُوكُمْ ۚ وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ ۚ وَلَا تُقَاتِلُوهُمْ عِندَ الْمَسْجِدِ الْحَرَ‌امِ حَتَّىٰ يُقَاتِلُوكُمْ فِيهِ ۖ فَإِن قَاتَلُوكُمْ فَاقْتُلُوهُمْ ۗ كَذَٰلِكَ جَزَاءُ الْكَافِرِ‌ينَ ﴿١٩١﴾ فَإِنِ انتَهَوْا فَإِنَّ اللَّـهَ غَفُورٌ‌ رَّ‌حِيمٌ ﴿١٩٢﴾ وَقَاتِلُوهُمْ حَتَّىٰ لَا تَكُونَ فِتْنَةٌ وَيَكُونَ الدِّينُ لِلَّـهِ ۖ فَإِنِ انتَهَوْا فَلَا عُدْوَانَ إِلَّا عَلَى الظَّالِمِينَ ﴿١٩٣﴾ الشَّهْرُ‌ الْحَرَ‌امُ بِالشَّهْرِ‌ الْحَرَ‌امِ وَالْحُرُ‌مَاتُ قِصَاصٌ ۚ فَمَنِ اعْتَدَىٰ عَلَيْكُمْ فَاعْتَدُوا عَلَيْهِ بِمِثْلِ مَا اعْتَدَىٰ عَلَيْكُمْ ۚ وَاتَّقُوا اللَّـهَ وَاعْلَمُوا أَنَّ اللَّـهَ مَعَ الْمُتَّقِينَ ﴿١٩٤﴾

2:190-194 Fight in the cause of God those who fight you, but do not transgress limits; for God loves not transgressors. And kill them wherever ye catch them, and turn them out from where they have turned you out; for persecution and oppression are worse than slaughter; but fight them not at the Sacred Mosque, unless they (first) fight you there; but if they fight you, kill them. Such is the reward of those who reject faith. But if they cease, God is Oft-Forgiving, Most Merciful. And fight them on until there is no more tumult or oppression, and there prevail justice and faith in God; but if they cease, let there be no hostility except to those who practice oppression. The prohibited month, for the prohibited month, and so for all things prohibited, there is the law of equality. If then any one transgresses the prohibition against you, transgress ye likewise against him. But fear (the punishment of) God, and know that God is with those who restrain themselves.

How many times do we see the above verse repeating the message to make it clear? These verse were revealed at a time when Muslims of Madinah were under constant attack from the Makkans. An example would be when the Makkans conducted the public crucifixion of the companion of the Prophet Muhammad (peace be upon him), Khubaib bin Adi. These would be classified as 'terrorist activities' according to the modern usage of the term. So what does this verse say in this context? "Fight in the cause of God those who fight you", "unless they (first) fight you there" - the context of this verse applies to those who initiate the attack against Muslims. And even after they attack, the verse makes it clear: "But if they cease, God is Oft-Forgiving, Most Merciful." And it also makes clear the purpose for what Muslims fight: "fight them on until there is no more tumult or oppression, and there prevail justice and faith in God". It is the duty of Muslims to defend humanity from oppression and persecution and to establish justice. Muslims believe that God has placed us here on earth as his deputy or viceroy, and thus, it is our duty to enjoin the good and forbid the evil, to establish peace and justice in the land. Dr. Maher Hathout writes the following on verses 2:190-194:

These verses were applicable to a particular situation or if, hypothetically, the same situation was to be repeated… Historically, fighting back against the aggressors was prohibited during the thirteen years of the Meccan period. After the migration to Medina and the establishment of the Islamic state, Muslims were concerned with how to defend themselves against aggression from their enemies. The aforementioned verses were revealed to enable them to protect the newly formed state by fighting in self-defence against those who fought them. However, the Qur’an clearly prohibits aggression. The verses explain that fighting is only for self-defence. Thus, a Muslim cannot commit aggression and kill innocent men, women, children, the sick, the elderly, monks, priests, or those who do not wish to fight. A Muslim is also mandated not to destroy plant life of livestock. (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, p.49, emphasis added)

The historical context is something that must always be considered where developing an understanding of Qur'anic verses. Without knowing the circumstances behind the revelation, one cannot apply the verse as accurately. Shaykh Salman Al-Oadah writes about the general principles in Jihad:

Jihad can never be fought for worldly gain, for conquest, or even for revenge. Muslims must only fight to protect the lives, property, and freedoms of people, especially their freedom to worship Allah when that freedom is forcibly attacked. They are never allowed to attack innocent people, even when they are themselves attacked by the countrymen of those innocents. Any people that go against this established principle of Islamic Law and murder civilians are fighting against Islam and everything that it stands for. It is ludicrous for them to call this fighting a jihâd, a word that means striving in the cause of Islam. They are in fact murderers in the light of Islamic Law and should be treated as such. (SOURCE, emphasis added)

There are strict and detailed laws in Islam, which Muslims must follow carefully. A military Jihad must be performed under these regulations. Abdullah Yusuf Ali writes about verse 2:190:

War is only permissible in self-defence, and under well-defined limits. When undertaken, it must be pushed with vigour, but not relentlessly, but only to restore peace and freedom for the worship of God. In any case strict limits must not be transgressed: women, children, old and infirm men should not be molested, nor trees and crops cut down, nor peace withheld when the enemy comes to terms. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary )

He then re-iterates the general principles behind Jihad in his commentary on verse 2:191:

In general, it may be said that Islam is the religion of peace, goodwill, mutual understanding, and good faith. But it will not acquiesce in wrong-doing, and its men will hold their lives cheap in defence of honour, justice, and the religion which they hold sacred. Their ideal is that of heroic virtue combined with unselfish gentleness and tenderness, such as is exemplified in the life of the Apostle. They believe in courage, obedience, discipline, duty, and a constant striving by all the means in their power, physical, moral, intellectual, and spiritual, for the establishment of truth and righteousness. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary )

This is the true focus behind Jihad, and Muslims must never lose this focus. Jihad is solely for the purpose of aiding humanity and bringing justice and freedom to the oppressed. Therefore, all actions must be in-line with this focus and the strict regulations governing Jihad. The focus is to defend, not destroy. One who focuses on the betterment and aid of humanity will realize that destruction will never achieve this. Abdul Majid Daryabadi writes extensively on verse 2:190:

2:190 “And fight in the way of Allah those who fight you” – Violating the truce they themselves had signed. The Muslims, after having borne untold persecution with almost superhuman fortitude for years and years at the hands of the pagans of Makkah, are now for the first time enjoined to take to reprisals. ‘For a full thirteen years the Muslims were subjected to relentless persecution in Mecca. The Prophet and his followers fled for life to Medina, but the enemy would not leave them alone in their refuge. They came to attack them within a year, and the first three battles were fought in the very locality which will whether the Prophet was an assailant or defendant’ (Headley, The Original Church of Jesus Christ and Islam, p. 155). The Makkans had signed a truce and were the first to break it. The words ‘fight with those who fight you’ clearly show, firstly, that the Muslims were not the aggressors, and secondly, that those of the enemy who were not actual combatants – children, women, monks, hermits, the aged and the infirm, the maimed, and the like – had nothing at all to fear from the Muslim soldiery. It was in light of this express Divine injunction that the great Abu Bakr, the first Caliph, charged his troops into Syria, ‘not to mutilate the dead, nor to slay old men, women, and children, nor to cut down fruit-trees, nor to kill cattle unless they were needed for food; and these humane precepts served like a code of laws of war during the career of Mohammadan conquest.’ (Bosworth Smith, Mohammed and Mohammedanism, p. 185). Has not Islam thus, in prescribing war against those who break God’s law, who challenge His righteous authority, and who fill the world with violence and injustice, made every concession short of the impossible? Has any code of military ethics been so chivalrous, so humane and so tender towards the enemy? ‘The moral tone adopted by the Caliph Abu Bakr, in his instructions to the Syrian army, was’, says a modern Christian historian, ‘so unlike the principles of the Roman government, that it must have commanded profound attention from a subject people. Such a proclamation announced to Jews and Christians’ sentiments of justice and principles of toleration which neither Roman emperors nor orthodox bishops had ever adopted as the rule of their conduct’ (Finlay, Greece Under the Romans, pp. 367-368). (Daryabadi, The Glorious Qur’an, emphasis added)

Muhammad Asad explains verse 2:190 in the following manner:

This and the following verses lay down unequivocally that only self-defence (in the widest sense of the word) makes war permissible for Muslims. Most of the commentators agree in that the expression la ta'tadu signifies, in this context, "do not commit aggression"; while by al-mu'tadin "those who commit aggression" are meant. The defensive character of a fight "in God's cause" - that is, in the cause of the ethical principles ordained by God - is, moreover, self-evident in the reference to "those who wage war against you", and has been still further clarified in 22: 39 - "permission [to fight] is given to those against whom war is being wrongfully waged" - which, according to all available Traditions, constitutes the earliest (and therefore fundamental) Quranic reference to the question of jihad, or holy war (see Tabari and Ibn Kathir in their commentaries on 22: 39). That this early, fundamental principle of self-defence as the only possible justification of war has been maintained throughout the Quran is evident from 60: 8, as well as from the concluding sentence of 4: 91, both of which belong to a later period than the above verse. (Asad, The Message of the Qur’an, emphasis added)

And on verse 2:191, he states the following:

In view of the preceding ordinance, the injunction "slay them wherever you may come upon them" is valid only within the context of hostilities already in progress (Razi), on the understanding that "those who wage war against you" are the aggressors or oppressors (a war of liberation being a war "in God's cause"). The translation, in this context, of fitnah as "oppression" is justified by the application of this term to any affliction which may cause man to go astray and to lose his faith in spiritual values (cf. Lisan al-Arab). (Asad, The Message of the Qur’an, emphasis added)

This extensive commentary on this verse should sufficiently address all confusion and misconceptions that resulted from misquoting this verse.

Quran 2:216 "Fighting is ordained for you..."

Quran 2:216 Jihad ['Qital'] (holy war in the cause of God) is ordained for you (Muslims), though you dislike it. But it is possible that you dislike a thing which is good for you, and like a thing which is bad for you. But God knows, and you know not.

كُتِبَ عَلَيْكُمُ الْقِتَالُ وَهُوَ كُرْ‌هٌ لَّكُمْ ۖ وَعَسَىٰ أَن تَكْرَ‌هُوا شَيْئًا وَهُوَ خَيْرٌ‌ لَّكُمْ ۖ وَعَسَىٰ أَن تُحِبُّوا شَيْئًا وَهُوَ شَرٌّ‌ لَّكُمْ ۗ وَاللَّـهُ يَعْلَمُ وَأَنتُمْ لَا تَعْلَمُونَ ﴿٢١٦﴾

The first mistake in this translation is that this Quranic verse actually does not use the word “Jihad”. This verse actually uses the word “Qital”, which refers to physical combat in war. Combat is ordained for Muslims in order to defend themselves and their rights, as well as the rights of others. The obligation to physically defend one’s rights, and to establish justice was elaborated on in the previously mentioned article on Jihad. It is sufficient to quote a verse from the Quran in this regard:

4:75 And what is wrong with you that you do not engage in combat for the sake of  Allah, and for those weak, ill-treated and oppressed among men, women, and children, whose cry is: "Our Lord! Rescue us from this town whose people are oppressors; and raise for us from You one who will protect, and raise for us from You one who will help."

وَمَا لَكُمْ لَا تُقَاتِلُونَ فِي سَبِيلِ اللَّـهِ وَالْمُسْتَضْعَفِينَ مِنَ الرِّ‌جَالِ وَالنِّسَاءِ وَالْوِلْدَانِ الَّذِينَ يَقُولُونَ رَ‌بَّنَا أَخْرِ‌جْنَا مِنْ هَـٰذِهِ الْقَرْ‌يَةِ الظَّالِمِ أَهْلُهَا وَاجْعَل لَّنَا مِن لَّدُنكَ وَلِيًّا وَاجْعَل لَّنَا مِن لَّدُنكَ نَصِيرً‌ا ﴿٧٥﴾

It is most certainly a duty of all human beings to help each other from oppression and injustice. This is what Islam teaches. Commenting on verse 2:216, Abdullah Yusuf Ali writes:

To fight (combat) in the cause of Truth is one of the highest forms of charity. What can you offer that is more precious than your own life? But here again the limitations come in. If you are a mere brawler, or a selfish aggressive person, or a vainglorious bully, you deserve the highest censure. (Yusuf Ali, The Holy Qur'an, Text, Translation and Commentary )

Therefore, the fighting ordained by God in the Qur'an is the fighting to establish justice and security in the land, and this is a duty upon all human beings. We will always hope for peace, but we must realize that without justice, freedom, rights and equity, peace will never be able to survive. Likewise, on verse 2:216, Abdul Majid Daryabadi writes:

War, it has been truly said, is sanctioned by the law of nature – the constitution of man and the constitution of society – and is at times a biological and sociological necessity. Islam, the ideal and practical religion has allowed it, but only in cases of sheer necessity. (Daryabadi, The Glorious Qur’an, emphasis added)

Islam has designated war as the last resort and only in cases of sheer necessity, in order for us to defend the rights of ourselves and others. Also, the picture becomes even more clear when we take into consideration the historical context of the revelation. Abdullah Yusuf Ali goes on to explain the historical context in his commentary on verse 2:217:

The intolerance and persecution of the Pagan clique at Mecca caused untold hardships to the holy Messenger of Islam and his early disciples. They bore all with meekness and long-suffering patience until the holy one permitted them to take up arms in self-defence… (Yusuf Ali, The Holy Qur'an, Text, Translation and Commentary )

In light of the above quote, it becomes apparent that fighting has been especially ordained in conditions of severe persecution and hardship. Consequently, the Muslims are required to defend themselves from oppression and establish justice. To abstain from helping those under oppression is cowardice. Abdul Majid Daryabadi also explains the historical context of the verse:

Persecuted, harassed, afflicted, poverty-ridden, exiled, and small in number as the Muslims were at the time of the enactment of warfare, it was but natural that they were none too fond of crossing swords with the mighty forces that had conspired for their extirpation. Nothing short of express and emphatic Divine Command could urge them on to the field of battle [in order to defend their rights]. And yet the Islamic jihads are declared to be ‘designed by the Prophet to satisfy his discontented adherents by an accession of plunder!’ (Margoliouth). Such is this European scholar’s love of veracity! Such is his wonderful reading of history! (Daryabadi, The Glorious Qur’an)

The commentary on this verse makes it very clear that Muslims have always understood this verse as the legal right to defend one’s rights from the forces of oppression, but never to transgress limits .

Quran 4:89 - But if they turn away, catch and slaughter them...

But if they turn away, catch them and slaughter them wherever ye find them; and (in any case) take no friends or helpers from their ranks." (4:89)

This verse has been misquoted like the previous verse, out of context. Here is the full passage:

فَمَا لَكُمْ فِي الْمُنَافِقِينَ فِئَتَيْنِ وَاللَّـهُ أَرْ‌كَسَهُم بِمَا كَسَبُوا ۚ أَتُرِ‌يدُونَ أَن تَهْدُوا مَنْ أَضَلَّ اللَّـهُ ۖ وَمَن يُضْلِلِ اللَّـهُ فَلَن تَجِدَ لَهُ سَبِيلًا ﴿٨٨﴾ وَدُّوا لَوْ تَكْفُرُ‌ونَ كَمَا كَفَرُ‌وا فَتَكُونُونَ سَوَاءً ۖ فَلَا تَتَّخِذُوا مِنْهُمْ أَوْلِيَاءَ حَتَّىٰ يُهَاجِرُ‌وا فِي سَبِيلِ اللَّـهِ ۚ فَإِن تَوَلَّوْا فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ وَجَدتُّمُوهُمْ ۖ وَلَا تَتَّخِذُوا مِنْهُمْ وَلِيًّا وَلَا نَصِيرً‌ا ﴿٨٩﴾ إِلَّا الَّذِينَ يَصِلُونَ إِلَىٰ قَوْمٍ بَيْنَكُمْ وَبَيْنَهُم مِّيثَاقٌ أَوْ جَاءُوكُمْ حَصِرَ‌تْ صُدُورُ‌هُمْ أَن يُقَاتِلُوكُمْ أَوْ يُقَاتِلُوا قَوْمَهُمْ ۚ وَلَوْ شَاءَ اللَّـهُ لَسَلَّطَهُمْ عَلَيْكُمْ فَلَقَاتَلُوكُمْ ۚ فَإِنِ اعْتَزَلُوكُمْ فَلَمْ يُقَاتِلُوكُمْ وَأَلْقَوْا إِلَيْكُمُ السَّلَمَ فَمَا جَعَلَ اللَّـهُ لَكُمْ عَلَيْهِمْ سَبِيلًا ﴿٩٠﴾ سَتَجِدُونَ آخَرِ‌ينَ يُرِ‌يدُونَ أَن يَأْمَنُوكُمْ وَيَأْمَنُوا قَوْمَهُمْ كُلَّ مَا رُ‌دُّوا إِلَى الْفِتْنَةِ أُرْ‌كِسُوا فِيهَا ۚ فَإِن لَّمْ يَعْتَزِلُوكُمْ وَيُلْقُوا إِلَيْكُمُ السَّلَمَ وَيَكُفُّوا أَيْدِيَهُمْ فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ ۚ وَأُولَـٰئِكُمْ جَعَلْنَا لَكُمْ عَلَيْهِمْ سُلْطَانًا مُّبِينًا ﴿٩١﴾

4:88-91 Why should ye be divided into two parties about the Hypocrites? Allah hath upset them for their (evil) deeds. Would ye guide those whom Allah hath thrown out of the Way? For those whom Allah hath thrown out of the Way, never shalt thou find the Way. They but wish that ye should reject Faith, as they do, and thus be on the same footing (as they): so take not friends from their ranks until they forsake the domain of evil in the way of God (from what is forbidden). But if they revert to [open] enmity, seize them and slay them wherever ye find them; and (in any case) take no friends or helpers from their ranks. Except those who join a group between whom and you there is a treaty (Of peace), or those who approach you with hearts restraining them from fighting you as well as fighting their own people. If God had pleased, He could have given them power over you, and they would have fought you: therefore if they withdraw from you but fight you not, and (instead) send you (guarantees of) peace, then God hath opened no way for you (to war against them). Others you will find that wish to gain your confidence as well as that of their people: every time they are sent back to temptation, they succumb thereto; if they withdraw not from you nor give you (guarantees) of peace besides restraining their hands, seize them and slay them wherever ye get them; in their case We have provided you with a clear argument against them

So in the same manner as the first verse, this verse also only commands Muslims to fight those who practice oppression or persecution, or attack the Muslims. And in the event of a battle, the same laws of war are in place and a Muslim who transgresses limits should prepare for the punishment of God. In response to a question on verses 4:88-89, Dr. Muzammil H. Siddiqi quotes the verses in their full context and then asks the following:

Now tell me honestly, do these verses give a free permission to kill any one anywhere? These verses were revealed by God to Prophet Muhammad (peace and blessings be upon him), at the time when Muslims were attacked by the non-Muslims of Makkah on a regular basis. They were frightening the Muslim community of Madinah. One may say using the contemporary jargon that there were constant terrorist attacks on Madinah and in this situation Muslims were given permission to fight back the “terrorist”. These verses are not a permission for “terrorism” but they are a warning against the “terrorists.” But even in these warnings you can see how much restraint and care is emphasized. (SOURCE, emphasis added)

It is also important to note that the Qur'an clearly condemns murder. The Qur’an says about the prohibition of murder,

6:151 Take not life, which God hath made sacred, except by way of justice and law: thus does He command you, that ye may learn wisdom. 17:33 Nor take life, which God has made sacred, except for just cause. And if anyone is slain wrongfully, We have given his heir authority (to demand Qisas(retribution) or to forgive): but let him not exceed bounds in the matter of taking life; for he is helped (by the law) 5:32...if any one slew a person - unless it be for murder or for spreading mischief in the land - it would be as if he slew the whole people: and if any one saved a life, it would be as if he saved the life of the whole people

So the Qur'an makes it very clear that Muslims cannot initiate an attack against others, unless there is an immediate threat of being attacked. The context of the quoted verses applies only to situations where the oppressors are killing Muslims. In this case, they have a right to defend themselves and others, especially the weak and oppressed.

Quran 5:51 Don't take Jews and the Christians as friends ?!

5:51 O ye who believe! take not the Jews and the Christians for your friends: They are but friends to each other. And he amongst you that turns to them is of them. Verily Allah guideth not a people unjust.

يَا أَيُّهَا الَّذِينَ آمَنُوا لَا تَتَّخِذُوا الْيَهُودَ وَالنَّصَارَ‌ىٰ أَوْلِيَاءَ ۘ بَعْضُهُمْ أَوْلِيَاءُ بَعْضٍ ۚ وَمَن يَتَوَلَّهُم مِّنكُمْ فَإِنَّهُ مِنْهُمْ ۗ إِنَّ اللَّـهَ لَا يَهْدِي الْقَوْمَ الظَّالِمِينَ ﴿٥١﴾

The first point to be noted is that, in the verse above, the word Awliya is often incorrectly translated as friends (Awliya is the plural and its singular is wali and the concept is walaah). As a result, many people are under the misconception that this verse commands Muslims to distance themselves from Non-Muslims and to avoid friendship with them. This is far from the truth, as we shall see after examining the meaning of the word Awliya.God in the  Qur'an says: 

[42:9] 

Or have they taken Awliya besides him? But Allah - He is the wali, and He gives life to the dead, and He is over all things competent.

أَمِ اتَّخَذُوا مِن دُونِهِ أَوْلِيَاءَ ۖ فَاللَّـهُ هُوَ الْوَلِيُّ وَهُوَ يُحْيِي الْمَوْتَىٰ وَهُوَ عَلَىٰ كُلِّ شَيْءٍ قَدِيرٌ‌ ﴿٩﴾ 

3:122 ...Allah was their WALI (protector), and in Allah should the faithful (Ever) put their trust.

وَاللَّـهُ وَلِيُّهُمَا ۗ وَعَلَى اللَّـهِ فَلْيَتَوَكَّلِ الْمُؤْمِنُونَ ﴿١٢٢﴾

This verse indicates that a wali is one in whom trust is placed for protection, as the Qur'an always declares God the protector, wali, of the righteous. As Dr. Saeed Ismail Sieny concludes his discussion on Walaah by writing:

As we have discovered above, the root of the word "al-walaah" does not include love, support, etc., and that the core meaning rests on guardianship. (Sieny, The Relationship Between Muslims and Non-Muslims; Toronto, Al-Attique Publishers Inc., 2000, p. 102, emphasis added)

And Dr. Muzammil Siddiqi writes:

In the verse you quoted, the word "Awliya" is used. It is a plural and its singular is "wali". The correct translation of the word ""wali"" is not "friend" but it is someone who is very close and intimate. It is also used to mean "guardian, protector, patron, lord and master". In the Qur'an this word is used for God, such as “Allah is the Protector (or Lord and Master) of those who believe. He takes them out from the depths of darkness to light…” (Al- Baqarah: 257)

اللَّـهُ وَلِيُّ الَّذِينَ آمَنُوا يُخْرِ‌جُهُم مِّنَ الظُّلُمَاتِ إِلَى النُّورِ‌ ۖ ... ﴿٢٥٧﴾

There are many other references in the Qur'an that give this meaning. The same word is also sometimes used in the Qur'an for human beings, such as
“And whosoever is killed unjustly, We have granted his next kin "wali" the authority (to seek judgment or punishment in this case)…”(Al-‘Isra' :33)
(SOURCE emphasis added)

وَمَن قُتِلَ مَظْلُومًا فَقَدْ جَعَلْنَا لِوَلِيِّهِ سُلْطَانًا فَلَا يُسْرِ‌ف فِّي الْقَتْلِ ۖ إِنَّهُ كَانَ مَنصُورً‌ا ﴿٣٣﴾

It becomes clear that the word Awliya cannot be taken as simply referring to friendship, as it contains a much more complex meaning, including dependence and guardianship. Therefore, a more accurate translation of the verse would be:

5:51 O ye who believe! take not the Jews and the Christians for your protectors: They are but protectors to each other. And he amongst you that turns to them is of them. Verily Allah guideth not a people unjust.

Therefore, the referred verse does not prohibit friendship with Non-Muslims at all. Dr. Muzammil Siddiqi writes:

The Qur'an does not say that non-Muslims cannot be Muslims' friends, nor does it forbid Muslims to be friendly to non-Muslims. There are many non-Muslims who are good friends of Muslim individuals and the Muslim community. There are also many good Muslims who truly and sincerely observe their faith and are very friendly to many non-Muslims at the same time. Islam teaches us that we should be friendly to all people. Islam teaches us that we should deal even with our enemies with justice and fairness. Allah says in the Qur'an in the beginning of the same Surah Al-Ma’dah: “O you who believe! Stand out firmly for Allah as witnesses to fair dealings and let not the hatred of others to you make you swerve to wrong and depart from justice. Be just, that is next to piety. Fear Allah, indeed Allah is well-acquainted with all that you do.” (Al-Ma’dah :8)
In another place in the Qur'an, Allah Almighty says:
“Allah forbids you not with regard to those who fight you not for your faith, nor drive you out of your homes, from dealing kindly and justly with them. For Allah loves those who are just. Allah only forbids you with regard to those who fight you for your faith, and drive you out of your homes and support others in driving you out, from turning to them for protection (or taking them as wali). Those who seek their protection they are indeed wrong- doers.” (Al-Mumtahinah: 8-9)

لَّا يَنْهَاكُمُ اللَّـهُ عَنِ الَّذِينَ لَمْ يُقَاتِلُوكُمْ فِي الدِّينِ وَلَمْ يُخْرِ‌جُوكُم مِّن دِيَارِ‌كُمْ أَن تَبَرُّ‌وهُمْ وَتُقْسِطُوا إِلَيْهِمْ ۚ إِنَّ اللَّـهَ يُحِبُّ الْمُقْسِطِينَ ﴿٨﴾ إِنَّمَا يَنْهَاكُمُ اللَّـهُ عَنِ الَّذِينَ قَاتَلُوكُمْ فِي الدِّينِ وَأَخْرَ‌جُوكُم مِّن دِيَارِ‌كُمْ وَظَاهَرُ‌وا عَلَىٰ إِخْرَ‌اجِكُمْ أَن تَوَلَّوْهُمْ ۚ وَمَن يَتَوَلَّهُمْ فَأُولَـٰئِكَ هُمُ الظَّالِمُونَ ﴿٩﴾

Moreover, Allah Almighty has described Prophet Muhammad, peace and blessings be upon him, as "a mercy" to the worlds. He was a sign of Allah's Mercy to all, Muslims as well as non-Muslims. In his kindness and fair treatment he did not make any difference between the believers and non-believers. He was kind to the pagans of Makkah and fought them only when they fought him. He made treaties with the Jews of Madinah and honored the treaties until they broke them. He, peace and blessings be upon him, is reported to have received the Christians of Najran with kindness in his Masjid in Madinah. They argued with him about Islam, but he returned them with honor and respect. There are many examples from his life that show that he was the friendliest person to all people. (SOURCE)

And as Muhammad Asad writes:

As regards the meaning of the "alliance" referred to here, see 3:28, and more particularly 4: 139 and the corresponding note, which explains the reference to a believer's loss of his moral identity if he imitates the way of life of, or-in Qur'anic terminology-"allies himself" with, non-Muslims. However, as has been made abundantly clear in 60: 7-9 (and implied in verse 57 of this Surah), this prohibition of a "moral alliance" with non-Muslims does not constitute an injunction against normal, friendly relations with such of them as are well-disposed towards Muslims. It should be borne in mind that the term wall has several shades of meaning: "ally", "friend", "helper", "protector", etc. The choice of the particular term - and sometimes a -combination of two terms-is always dependent on the context. (Asad, The Message of the Qur’an, emphasis added)

The second point to note is that although this verse makes a general statement, the ruling is specific and is to be applied in a context similar to the historical context. Shaykh Yusuf Al-Qaradawi wrote about this topic extensively in response to a similar question:

[The answer to this is that these verses are not unconditional, to be applied to every Jew, Christian, or non-Muslim. Interpreting them in this manner contradicts the injunctions of the Qur'an which enjoin affection and kindness to the good and peace-loving peoples of every religion, as well as the verses which permit marriage to the women of the People of the Book, with all that Allah says concerning marriage and He has put love and mercy between you” (30:21)
and the verse concerning the Christians:
And thou wilt find those who say, 'Surely we are Christians,' to be nearest to them (the Muslims in affection...(5:82)
The verses cited above [verse 5:51] were revealed in connection with those people who were hostile to Islam and made war upon the Muslims. Accordingly, it is not permissible for the Muslims to support or assist them - that is, to be their ally- nor to entrust them with secrets at the expense of his own religion and community. This point is explained in other verses, in which Allah, The Most High, says:
They will spare nothing to ruin you; they yearn for what makes you suffer. Hatred has been expressed by their mouths, but what their hearts conceal is still greater. Thus have We made clear to you the revelations (or signs), if you possess understanding. Ah! You love them, but they do not love you…(3:118-119)
This ayah throws light on the character of such people, who conceal great enmity and hatred against the Muslims in their hearts and whose tongues express some of the effects of such hostility. (Al-Qaradawi, Al-Halal Wal Haram Fil Islam; US American Trust Publications, 1994, p. 340, emphasis added)

As Shaykh Qaradawi mentioned, verse 5:11 cannot possibly be taken as a prohibition of friendship since the Qur’an allows Muslim men to marry women from the People of the Book:

5:5 … virtuous women of the believers and the virtuous women of those who received the Scripture before you are lawful for you…

And the Qur’an describes the relationship of marriage to be a relationship with the deepest bond of love:

30:21 And among His Signs is this, that He created for you mates from among yourselves, that ye may dwell in tranquility with them, and He has put love and mercy between your (hearts): verily in that are Signs for those who reflect.

Also note that the Qur’an says:

60:8-9 Allah does not forbid you respecting those who have not made war against you on account of [your] religion, and have not driven you forth from your homes, that you show “Birr” with them and deal with them justly; surely Allah loves the doers of justice. Allah only forbids you respecting those who made war upon you on account of [your] religion, and drove you forth from your homes and backed up [others] in your expulsion, that you make friends with them, and whoever makes friends with them, these are the unjust.

The word “birr” is the same word used to describe a Muslim’s relationship with their parents which is considered the most sacred blood relationship in Islam. Therefore, Muslims are clearly commanded to deal with peaceful non-Muslims is a friendly and peaceful manner. The third point is that the specific groups being referred to in this verse were those hostile to Islam, and not all Jews and Christians in general. Concerning the historical context, the verse was revealed during a time when the Muslims were being attacked from many directions, including the Christian Roman empire and the Jews of Madinah. The Muslims had originally made a pact with the Jews of Madinah, but they were betrayed twice. So in this context, the Qur'an was telling the believers to be cautious in dealings with such enemies who oppose Islam, and not to trust them as protectors. As Jasser Auda writes:

It was revealed in certain historic circumstances, in which there was a war between the infant Islamic state on different occasions on four different fronts: the Romans, the Persians, the pagans of Arabia, and the Jews of Madinah. So, the historic context of the revelation of this verse is a situation of war between Muslims and the People of the Book (Jews, internally in Madinah, and Christians, through a Roman crusade). So, yes, Muslims were not allowed to make friends with the enemies who were fighting them and wishing to eliminate them from the face of the earth. Some Muslims say that since the verse has this historic context, then it is part of history and no longer applies. This is not correct! It is true that the verse has a history behind it, but this does not mean that it is no longer relevant. It is totally relevant but only in a context similar to the historic context. So today Muslims are not to make friends with Jews or Christians (or followers of any other religion for that matter) if they try to kill Muslims, kick them out of their homes, etc. (SOURCE)

The Qur'anic verse is relevant in a similar context to the historical context. A Muslim cannot take Jews or Christians or anyone as protectors if they oppose their religion and its teachings. The Muslims are encouraged to rely on each other for support. Dr. Muzammil Siddiqi writes:

It is obvious that Jews patronize the Jews and Christians patronize the Christians, so why not Muslims patronize Muslims and support their own people. This verse is not telling us to be against Jews or Christians, but it is telling us that we should take care of our own people and we must support each other. In his Tafsir, (Qur’an exegesis) Imam Ibn Kathir has mentioned that some scholars say that this verse (i.e. the one you referred to) was revealed after the Battle of Uhud when Muslims had a set back. At that time, a Muslim from Madinah said, "I am going to live with Jews so I shall be safe in case another attack comes on Madinah." And another person said, "I am going to live with Christians so I shall be safe in case another attack comes on Madinah." So Allah revealed this verse reminding the believers that they should not seek the protection from others, but should protect each other. (See Ibn Kathir, Al-Tafsir, vol. 2, p. 68) (SOURCE)[/

The groups prohibited for Muslims to take as protectors are described in the Qur’an:

The Holy Qur'an, 60:1 O ye who believe! Take not my enemies and yours as protectors,- offering them (your) love, even though they have rejected the Truth that has come to you, and have (on the contrary) driven out the Prophet and yourselves (from your homes), (simply) because ye believe in Allah your Lord! If ye have come out to strive in My Way and to seek My Good Pleasure, (take them not as friends), holding secret converse of love (and friendship) with them: for I know full well all that ye conceal and all that ye reveal. And any of you that does this has strayed from the Straight Path. 60:2 If they were to get the better of you, they would behave to you as enemies, and stretch forth their hands and their tongues against you for evil: and they desire that ye should reject the Truth.

يَا أَيُّهَا الَّذِينَ آمَنُوا لَا تَتَّخِذُوا عَدُوِّي وَعَدُوَّكُمْ أَوْلِيَاءَ تُلْقُونَ إِلَيْهِم بِالْمَوَدَّةِ وَقَدْ كَفَرُ‌وا بِمَا جَاءَكُم مِّنَ الْحَقِّ يُخْرِ‌جُونَ الرَّ‌سُولَ وَإِيَّاكُمْ ۙ أَن تُؤْمِنُوا بِاللَّـهِ رَ‌بِّكُمْ إِن كُنتُمْ خَرَ‌جْتُمْ جِهَادًا فِي سَبِيلِي وَابْتِغَاءَ مَرْ‌ضَاتِي ۚ تُسِرُّ‌ونَ إِلَيْهِم بِالْمَوَدَّةِ وَأَنَا أَعْلَمُ بِمَا أَخْفَيْتُمْ وَمَا أَعْلَنتُمْ ۚ وَمَن يَفْعَلْهُ مِنكُمْ فَقَدْ ضَلَّ سَوَاءَ السَّبِيلِ ﴿١﴾

So the Qur'an forbids taking those as protectors who expel the Muslims from their homes and who would betray and attack as soon as the opportunity arises. Those who have no respect for a Muslim’s beliefs and desire that the Muslim leaves their faith - they cannot be taken as protectors. This is the correct interpretation based on the context of the verse. To conclude, we once again quote Dr. Muzammil Siddiqi:

Muslims are allowed to have non-Muslims as friends as long as they keep their own faith and commitment to Islam pure and strong. You are correct in pointing out that a Muslim man is also allowed to marry a Jewish or Christian woman. It is obvious that one marries someone for love and friendship. If friendship between Muslims and Jews or Christians was forbidden, then why would Islam allow a Muslim man to marry a Jew or Christian woman? It is the duty of Muslims to patronize Muslims. They should not patronize any one who is against their faith or who fights their faith, even if they were their fathers and brothers. Allah says: “O you who believe! Take not for protectors (Awliya') your fathers and your brothers if they love unbelief above faith. If any of you do so, they are indeed wrong-doers.” (Al-Tawbah : 23)
In a similar way, the Qur'an also tells Muslims that they should never patronize the non-Muslims against other Muslims. However, if some Muslims do wrong to some non-Muslims, it is Muslim’s duty to help the non-Muslims and save them from oppression . The Prophet, peace and blessings be upon him, said that he himself will defend a Dhimmi living among Muslims to whom injustice is done by Muslims. But Islam also teaches that Muslims should not seek the patronage of non-Muslims against other Muslims. They should try to solve their problems among themselves. (SOURCE)

Islam is a religion of peace and compassion, therefore it requires its adherents to act in the best possible manner to other human beings. Verse 5:51 does not refer to friends, but protectors, and the historical context reveals that this verse prohibits Muslims from seeking the protection and allegiance of those who are hostile to the Islamic faith. It is not a reference to all Non-Muslims, as the scholars of Islam have clarified.

Footnote:

 Can Christians Befriend Non-Christians?:

The answer from www.gotquestions.org:
http://www.gotquestions.org/friendships-unbelievers.html