This article was originally taken from the following site: discover-the-truth.com
This article seeks to examine chapter 9, verse 5 of the Quran in its historical context. Some claim that the verse ‘sanctions the killing of innocent people’, and this is how it was implemented by Prophet Mohammed (p). We shall respond to these claims in this piece.
The verse (9:5) is one of the most misquoted by opponents who want to paint the Islamic faith negatively. Whenever the verse is cited, it is sliced to pieces.
“…then slay the idolaters wherever you find them…” – Quran 9:5
From historical persepective, the reports (Ibn Ishaq and Tabari), and exegesis inform us that these verses were directly revealed concerning the polytheists of Arabia (Tafsir Ibn Kathir , Tafsir Jalalayn , As-Sawi  and Tanwir al-Miqbas min Tafsir Ibn ‘Abbas ). To recap, in the sixth year of Hijri the Muslims and the idolaters made a treaty. Part of the treaty was that neither parties would attack the other, nor would they attack any of their allies. This they agreed and went their ways. It didn’t take long when the Banu Bakr tribe (who were an ally of Quraysh) attacked and killed many of Banu Khuza’a tribe (they were allies of the Muslims). The Quraysh being in the middle, the Muslims would have presumed that they would have tried to stop their ally (Banu Bakr) attacking and killing Banu Khuza’a. However, historical reports inform us that the polytheistic Quraysh supported banu Bakr with weapons and their members also partook in killing Banu Khuza’a. From historical point of view, we see that the Quraysh were the first to breach the terms of the treaty.
The Prophet Muhammed (p) receiving news of what Banu Bakr and Quraysh idolaters did, he and his Companions assembled an army to march against them. It was on this occasion that the Muslims conquered Makkah (Tafsir Anwarul bayan).
NOTE: Although Surah Tawbah (Surah Bara’ah) mostly was revealed after the conquest of Makkah, however, these verses cited in this article (below) were revealed before that:
“‘Ruhul Ma’ani’ writes that although Surah Bara’ah was revealed after the conquest of Makkah, these verses were revealed before.” (Ruhul Ma’ani, volume 10 page 62). 
9:1 (This is a declaration of) immunity by Allah and His Messenger towards those of the idolaters with whom you made an agreement
9:2 So go about in the land for four months and know that you cannot weaken Allah and that Allah will bring disgrace to the unbelievers.
9:3 And an announcement from Allah and His Messenger to the people on the day of the greater pilgrimage that Allah and His Messenger are free from liability to the idolaters; therefore if you repent, it will be better for you, and if you turn back, then know that you will not weaken Allah; and announce painful punishment to those who disbelieve.
9:4 Except those of the idolaters with whom you made an agreement, then they have not failed you in anything and have not backed up any one against you, so fulfill their agreement to the end of their term; surely Allah loves those who are careful (of their duty).
9:5 So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush, then if they repent and keep up prayer and pay the poor-rate, leave their way free to them; surely Allah is Forgiving, Merciful.
9:6 And if one of the idolaters seek protection from you, grant him protection till he hears the word of Allah, then make him attain his place of safety; this is because they are a people who do not know.
9:7 How can there be an agreement for the idolaters with Allah and with His Messenger; except those with whom you made an agreement at the Sacred Mosque? So as long as they are true to you, be true to them; surely Allah loves those who are careful (of their duty).
9:8 How (can it be)! while if they prevail against you, they would not pay regard in your case to ties of relationship, nor those of covenant; they please you with their mouths while their hearts do not consent; and most of them are transgressors.
9:9 They have taken a small price for the communications of Allah, so they turn away from His way; surely evil is it that they do.
9:10 They do not pay regard to ties of relationship nor those of covenant in the case of a believer; and these are they who go beyond the limits.
9:11 But if they repent and keep up prayer and pay the poor-rate, they are your brethren in faith; and We make the communications clear for a people who know.
9:12 And if they break their oaths after their agreement and (openly) revile your religion, then fight the leaders of unbelief– surely their oaths are nothing– so that they may desist.
9:13 What! will you not fight a people who broke their oaths and aimed at the expulsion of the Messenger, and they attacked you first; do you fear them? But Allah is most deserving that you should fear Him, if you are believers.
9:1 – In the first verse we are informed that there was a treaty which the Quraish (and other tribes) broke, except the Banu Kinanah tribe who stayed faithful (Tanwir al-Miqbas min Tafsir Ibn ‘Abbas).
9:2 – The idolaters are told that they can go about freely in the land for four months, once the timing comes they will be dealt with, 1400 years ago.
9:3 – For breaking their treaty, God Almighty is inviting them to repent and turn away from the hostilities. Their plots do not in any way weaken God. There will be a punishment for those who broke the treaty and continue with their aggression.
9:4 – The punishment which the Muslims would have inflicted were only aimed at those who actively took up arms against the Muslims and broke the pact. This verse shows that the idolaters that were at peace and weren’t siding with the enemy were left alone. In Fact, God Almighty commands Muslims to fulfil their agreement with them and leave them be at peace since they have done nothing wrong against them (Tafsir al-Jalalayn, Tanwir al-Miqbas min Tafsir Ibn ‘Abbas and Tafsir Ibn Kathir).
9:5 – The end of the four months, and the slaying of the idolaters, refers to those who broke the treaty, and fought against the Muslims. As the previous verse showed, not all idolaters were fought against. Only those who broke the treaty and actively participated in warfare were dealt with.
9:6 – Even those idolaters who actively fought the Muslims, if they were to ask ‘protection’ from the Muslims, God Almighty commanded the believers to protect them and take them to a safe place so that they may hear the Words of the Quran. From this verse we can see that those who wanted peace and stopped their hostilities, after hearing the recitation of the Quran – they were allowed to go freely anywhere they wished. They were not forced to convert to Islam (Tanwir al-Miqbas min Tafsir Ibn ‘Abbas, Tafsir al-Jalalayn and Tafsir Ibn Kathir).
9:7 – How can there be an agreement with the idolaters when they have broken pacts and fought the Muslims many times. The only agreement that is still binding are those who didn’t break the treaty. Those who didn’t fight the Muslims, their treaty was still binding. The Muslims are ordered by God to stay true to the agreement with those who stayed faithful (Tanwir al-Miqbas min Tafsir Ibn ‘Abbas).
9:8 – This verse is in reference to those who broke the pact and waged war against the Muslims, as explained before. The verse informs us, how can they have a pact when they get an upper hand against the Muslims, they would not hesitate to break the pact and attack the Muslims without hesitation. In short, it shows how treacherous and warlike these people were who the Muslims were up against (Tafsir al-Jalalayn and Tanwir al-Miqbas min Tafsir Ibn ‘Abbas).
9:9 – The disbelievers of Makkah forcefully prevented people believing in the message of Islam (Tafsir al-Jalalayn, Tanwir al-Miqbas min Tafsir Ibn ‘Abbas and Tafsir Ibn Kathir).
9:10 – Here in the verse we are told that these treacherous folk do not respect ties of kinship nor any treaty. They are truly transgressors (Tafsir al-Jalalayn and Tanwir al-Miqbas min Tafsir Ibn ‘Abbas).
9:11 – If some of those who were at war with the Muslims repented from their past transgressions, prayed, pay zakat (poor-rate), they are brothers of the Muslims (Tafsir al-Jalalayn and Tanwir al-Miqbas min Tafsir Ibn ‘Abbas). A reminder to readers, those that did become Muslim, done so freely. Forced conversion in Islam is Haram (forbidden).
9:12 – Although the verse says to fight those who broke the pact and openly revile Islam. The previous verses (and Q. 9:13) show that breaking the pact and reviling Islam was not the only crime these people committed. As shown before, they also physically fought the Muslims (Khuza’a). The very next verse (9:13) clearly tells us that they attacked the Muslims (Banu Khuza’a).
9:13 – Here God says to the Muslims, why is it that you will not fight those idolaters who broke their oaths, aimed to expel Prophet Muhammed (p), and attacked the Muslims first (Tafsir al-Jalalayn and Tanwir al-Miqbas min Tafsir Ibn ‘Abbas). It seems from the verse that some of the Prophet’s companions, were unwilling to fight these warmongers.
Where we have addressed the verses one by one, we can see the textual context for the verses alone show that the Muslims were only fighting the idolaters as a result of them (1) breaking their treaty, (2) tried expelling the Prophet – (3) fought, and attacked the Muslims (Banu Khuza’ah). Furthermore, in light of the aforementioned information, we would like to add that majority of earliest scholars like Ibn Abbas (619 – 687 AD), a companion of Prophet Muhammed, Ata b. Abi Rabah (653 – 732 AD), Mujahid b. Jabr (645 – 722 AD), and Muqatil b. Sulayman (d. 767 AD) and later exegete like Fakhr al-Din al-Razi (1149 – 1209 AD) forbade initiation of military attacks and used surah 2:190 as proof.
Professor Asma Asfaruddin:
“… early exegetes and Jurists like Ibn Abbas, Ata b. Abi Rabah, Mujahid b. Jabr, and Muqatil b. Sulayman and later exegetes like Fakhr al-Din al-Razi firmly maintained that Qur’an 2:190 unambiguously forbade the initiation of military hostilities and that military activity could ony be launched against actual, not potential, combatants. …” 
“Then this ayat was revealed, meaning that it is lawful for you to fight if the unbelievers fight you. So the ayat is connected to the prior mention of hajj and entering houses by the back door. After this the Prophet fought those who fought him and refrained from those who refrained from fighting him until the ayat in Surat at-Tawba (9:5) was revealed, ‘Fight the idolaters,’… Ibn Abbas, Umar Ibn Abd’l – Aziz and Mujahid said that it is an ayat whose judgement REMAINS OPERATIVE and means: ‘FIGHT THOSE WHO FIGHT YOU and do not transgress by killing women, Children, monks and the like,’ as will be explained. An-Nahhas said that THIS IS THE SOUNDER POSITION IN TERMS OF BOTH THE SUNNA AND IN TERMS OF LOGIC. As for the Sunna, there is a Hadith reported by Ibn Ibn Umar that, during one of his expeditions the Messenger of Allah, saw a woman who had been killed and he ABHORRED THAT and FORBADE the killing of women and children. As for logic, it applies to children and those like them, like Monks, the chronically ill, old men and hirelings who clearly should not be killed. When Abu Bakr sent Yazid Ibn Abi Sufwan to Syria, he commanded that he should not do harm to certain groups. Malik and others transmitted this. …” 
Although we touched upon Surah 9:6 briefly, it needs further clarification. Some individuals are fond of twisting the verse to mean something it was never intended to say. It is claimed that the polytheists were forced to convert to Islam or faced the sword. This claim, historically speaking is simply not true.
The seemingly all-out war verse (9:5) when we look at the verse that follows (9:6) it shows opposite of what Surah 9:5 seems to convey. The classical commentators of the Quran say that 9:6 refers to all people who want to ask for protection. Hence, if the idolaters who were at war, stopped their hostilities and asked the Muslims then to hear the message of the Quran, and later rejected Islam. The Muslims were commanded by God to take them to a place of safety i.e., they were not killed even when they rejected Islam. This verse alone shows, the Muslims then were only fighting as a result of Quraysh’s aggression and hostilities, not for their beliefs.
Mujahid Ibn Jabr (645 – 722 AD):
“…this verse guarantees the safety of people in general (insan) who came to listen to the Prophet recite from the Qur’n until they had returned to the place of refuge whence they came.” 
9th Century scholar Hud b. Muhakkam:
“…the polytheists who requests safe conduct from Muslims in order to listen to the word of God is to be so granted and returned unharmed to his place of origin, whether he embraces Islam or not. This was the view of Mujahid, for example. Al-Kalbi is quoted as saying that the verse referred instead to a group of polytheists who wished to renew their pact with Muhammad asked them to profess Islam, offer prayers, and pay the zakat, they refused, and the Prophet LET THEM RETURN SAFELY TO THEIR HOMES. Ibn Muhakkam further notes that al-Hasan al-Basri had remarked thus on the status of this verse: ‘It is valid and unabrogated (muhkama) until the Day of Judgement.’” 
Al-Tabari (838 – 923 AD):
“…in this verse God counsels Muhammad, ‘If someone from among the polytheists (al-Mushrikun) – those whom I have commanded that you fight and slay after the passage of the sacred months – were to ask you, O Muhammad, for safe conduct in order to listen to the word of God, then grant this protection to him so that he may hear the word of God and you may recite it to him.’ Such an individual, according to the verse, is to be subsequently ESCORTED BACK TO HIS PLACE OF SAFETY EVEN IF HE REJECTS ISLAM AND FAILS TO BELIEVE AFTER THE PROPHET’S RECITATION OF THE QUR’AN BEFORE HIM. SCHOLARS IN THE PAST WHO HAVE AGREED WITH THIS GENERAL INTERPRETATION INCLUDE IBN ISHAQ, AL-SUDDI, AND MUJAHID…” 
Al-Wahidi (d. 1075 AD):
“…should someone from among the same group of polytheists request safe conduct and refuge among Muslims so that he may listen to the word of God and learn of its positive commandments and interdictions, he is to be so granted and escorted back to a place of safety. This is so because they are an ignorant people, and so should be given protection and the opportunity to acquire knowledge and perhaps submit to Islam.” 
Al-Zamakhshari (1070 – 1143 AD):
“…if one of the polytheists, with whom no pact (mithaq) exists, were to request safe conduct from the Muslims in order to listen to the Qur’an, then he should be granted it so that he may reflect God’s words. AFTERWARD, HE IS TO BE ESCORTED BACK TO HIS HOME WHERE HE FEELS SAFE. This, al-Zamakhshari says, is established practice for all time. Al-hasan al-Basri had similarly maintained that this verse is ‘valid till the day of resurrection.’ …” 
Al-Razi (1149 – 1209 AD):
“on the authority of Ibn Abbas, who relates that a polytheist man asked Ali b. Abi talib, ‘if we wished to approach the Messenger after the end of this period (the four sacred months) in order to listen to the word of God or for some other reason, will we be killed?’ Ali replied in the negative and recited this verse, affirming the granting of safe conduct to him so that he may listen to the Qur’an. … al-Razi further comments that this verse indicates that imitation of precedent (al-taqlid) is not sufficient in religion, and that critical inquiry (al-nazar) and the seeking of proofs (al-istidlal) are indispensable requirements within religion.
If emulation of precedent were enough, he argues, then this verse would not have granted a respite to this unbeliever, and would have been merely given a choice between professing his belief [In Islam] or death. As this did not occur, it confirms that Muslims are required to offer safe conduct to such person and thereby assuage his fears and allow him the opportunity to deliberate upon the proofs of religion. How long such a respite should last is not known; perhaps it should be determined according to the prevalent custom (bi-l-urg), he says.” 
Tanwir al-Miqbas min Tafsir Ibn ‘Abbas (d. 1414 AD) states that Prophet Muhammed granted safe passage to any of the idolaters who asked for it. So that they may hear the Quran. If he does not believe (i.e., embrace Islam), then he is to be left alone and granted safe passage back to the land he come from:
(And if anyone of the idolaters seeketh thy protection (O Muhammad), then protect him so that he may hear the word of Allah) so that he may hear your recitation of the words of Allah; (and AFTERWARD CONVEY HIM TO HIS PLACE OF SAFETY) TO THE PLACE HE IS GOING, IF HE REMAINS AN UNBELIEVER. (That) which I have mentioned (is because they are a folk who know not) Allah’s command and His divine Oneness. (Tanwir al-Miqbas min Tafsir Ibn ‘Abbas on Surah 9:6 online Source)
Tafsir al-Jalalayn also emphasizes that they were left alone if they didn’t believe in Islam, and were taken to their place of safety:
And if any one of the idolaters (ahadun, ‘one’, is in the nominative because of the [following] verb [istajāraka, ‘seeks your protection’] that validates it) seeks your protection, requests security from you against being killed, then grant him protection, provide security for him, SO THAT HE MIGHT HEAR THE WORDS OF GOD — THE QUR’AN — AND AFTERWARD CONVEY HIM TO HIS PLACE OF SECURITY, THAT IS, THE DWELLING-PLACES OF HIS FOLK, IF HE DOES NOT BELIEVE, SO THAT HE MIGHT REFLECT UPON HIS SITUATION — that, which is mentioned, is because they are a people who do not know, the religion of God, and so they must [be made to] hear the Qur’ān in order to [come to] know [religion]. (Tafsir al-Jalalayn on Surah 9:6 – Online source)
Classical Commentaries: Quraysh Initiated War
It is interesting to note, although some of the classical exegesis emphasized on offensive Jihad and used 9:5 as evidence. They themselves acknowledged in their commentaries that the verse was revealed as a consequence of the Quraysh (Banu Bakr) initiating war first. From their exegesis, they say that Prophet Muhammed (p) nor his companions initiated war against the idolaters. It was the Quraysh with Banu Bakr who provoked – led the Muslims to retaliate against them. Sadly this important information is always left out by those who want to paint the Islamic faith negatively. Let’s now read what the exegesis say.
Ibn Kathir (1301 – 1373 AD):
(then stand you true to them. Verily, Allah loves those who have Taqwa.) The Messenger of Allah and the Muslims preserved the terms of the treaty with the people of Makkah from the month of Dhul-Qa`dah in the sixth year of Hijrah, until the Quraysh broke it and helped their allies, Banu Bakr, against Khuza`ah, the allies of Allah’s Messenger . Aided by the Quraysh, Banu Bakr killed some of Bani Khuza`ah in the Sacred Area! The Messenger of Allah led an invasion army in the month of Ramadan, of the eighth year, and Allah opened the Sacred Area for him to rule over them…” (Tafsir Ibn Kathir on Surah 9:7, Online Source).
“It was also said that these Ayat refer to the idolators breaking the peace agreement with Muslims and aiding Bani Bakr, their allies, against Khuza`ah, the ally of the Messenger of Allah. This is why the Messenger of Allah marched to Makkah in the year of the victory, thus conquering it…” (Tafsir Ibn Kathir on Surah 9:13 – Online Source).
(except for those you made a treaty with at the Masjid al-Haram) Referring to the Treaty of Hudaybiyya. They are the Quraysh who were exempted before. (As long as they are straight with you, be straight with them) i.e. as long as they carry out the treaty and do not break it, you should fulfill it. The ma is conditional and not adverbial. (Allah loves those who have taqwa) The Prophet was straight in his treaty with them until they broke it by helping the Banu Bakr against Khuza’a. (Tafsir al-Jalalayn on Surah 9:7 – Online source)
“Will you not (a-la, ‘will not’ or ‘is not’, denotes incitement) fight a people who broke, violated, their oaths, their pacts, and intended to expel the Messenger, from Mecca — for they discussed this between them in their council assembly — initiating, combat, against you first?, when they fought alongside Banu Bakr against Khuza‘a, your allies? So what is stopping you from fighting them? Are you afraid of them? God is more worthy of your fear, when you fail to fight them, if you are believers.” (Tafsir al-Jalalayn on Surah 9:13, Online source)
“[ As-Sawi: This refers to the Treaty of al-Hudaybiyya which stipulated that there would be no war for twenty years. The Banu Bakr formed an alliance with Quraysh and the Khuza’a with the Prophet. Banu Bakr then attacked Khuza’a and Quraysh helped them with weapons, thus breaking the treaty. ‘Amr b. ‘Allam al-Khuza’i went and informed the Prophet what had happened. The Prophet said, “You will not be helped if I do not help you,” and made preparations and went to Makka and conquered it in 8 AH. …”(Tafsir as-Sawi on Surah 9:3 – Online source)
Tanwir al-Miqbas min Tafsir Ibn ‘Abbas:
“(Will ye not fight a folk) why is it that you do not fight a people, i.e. the people of Mecca (who broke their solemn pledges) which are between them and you, (and purposed to drive out the messenger) and wanted to kill the Messenger when they entered Dar al-Nadwah (and did attack you first) by breaking their pledge when they helped the Banu Bakr, their allies, against the Banu Khuza’ah, the allies of the Prophet (p)? (What! Fear ye them?) O believers, do you fear fighting them? (Now Allah hath more right that you should fear Him) because of leaving His command, (if ye are believers).” (Tanwir al-Miqbâs min Tafsir Ibn ‘Abbas on Surah 9:13 – Online Source)
Imam Ibn Qayyim al-Jawziyya (1292 – 1350 AD) commenting on Quran 9:7,
“When God sent His Apostle (p), most of the followers of these religions responded to him and to his successsors, voluntarily and willingly. NOBODY WAS COMPELLED TO DO SO. The Apostle fought only those who fought and waged war against him. He did not fight those who made peace with him, neither did he fight those who were under the pledge of truce. He was obeying the bidding of God Most Sublime were he said:
‘Let there be no compulsion in Religion: Truth stands out clear from error: whoever rejects Evil and believes in God hath grasped the most trustworthy hand-hold, that never breaks, and God heareth and knowth all things ‘ (al-Baqarah: 256).
The Apostle did not compel anyone to adopt Islam. The above quoted verse from the Qur’an negates compulsion in the sense of prohibition that is: do not compel a soul to embrace the Religion. The verse (Sura) was revealed to admonish some of the men among the companions whose children embraced Judaism and Christianity before the advent of Islam, and where with the advent of Islam, their fathers embraced the religion of Muhammad and attempted to compel their children to follow their lead. God Most Exalted prohibited the fathers from resorting to compulsion to inspire their children to embrace Islam out of their choice. … To him who ponders over the biography of the Prophet (p) it becomes clear that he did not compel anyone to embrace his religion, and that he only fought those who fought him. He did not fight those who made truce with him as long as they kept and honoured the truce. He never broke a promise, for God Most High bid him to fulfil his promises to them as long as they kept theirs. A propos, God Most Exalted said:
‘How can there be a league before God and His apostle, with the pagans, except thoe with whom ye made a treaty near the Sacred Mosque? As long as these stand true to you, stand ye true to them for God doth love the righteous’ (al-Tawbah: 7).
… Likewise, when the Prophet Muhammad made truce with (the tribe of) Quraysh holding for ten years, HE DID NOT START ANY FIGHT WITH THEM; BUT WHEN THEY VIOLATED THE MUTUAL AGREEMENT AND RAISED ARMS AGAINST HIM, HE FOUGHT BACK… he stopped the fight when they retreated and went off. The point is that he did not compel anyone at all to embrace his religion; but people embraced his religion voluntarily and willingly. When most of the people earth realized the True Guidance, and that he is genuinely the Apostle of God, they embraced his call. 
From the above classical commentaries we read that it was Banu Bakr and Quraysh idolaters who waged war. Which led to the Muslims assembling an army against them.
As part of this article, we are also going to provide scholarly contemporary commentaries for Surah 9:5, to get a better understanding.
Professor Asma Afsaruddin:
“…The Qur’an further asserts that it is the duty of Muslims to defend those who are oppressed and who cry out to them for help (4;75), except against a people with whom the Muslims have concluded a treaty (8:72). With regard to initiation of hostilities and conduct during war (jus in bello), the Quran has specific injunctions. Verse 2:190, which reads, ‘Fight in the cause of God those who fight you, but do not commit aggression, for God loves not aggressors,’ forbids Muslims from initiating hostilities.
Recourse to armed combat must be in response to a prior act of aggression by the opposite side. The Qur’an further counsels (5:8), ‘Let not rancor towards others cause you to incline to wrong and depart from justice. Be just; that is closer to piety.’ This verse may be understood to complement 2:190 in spirit and intent, warning against excesses that may result from an unprincipled desire to punish and exact revenge. During the month of Ramadan in the third year of the Islamic calendar (624 CE), full-fledged hostilities broke out between the Muslims and the pagan Meccans in what became known as the battle of Badr. In this battle, a small army of Muslims decisively routed a much larger and more experienced Meccan army. Two years later, the battle of Uhud was fought, in which the Muslims suffered severe reverses, followed by the battle of Khandaq in 627. Apart from these three major battles, a number of other minor campaigns were fought until the Prophet’s death in 632. Some of the most trenchant verses exhorting the Muslims to fight were revealed on the occasions of these military campaigns. One such verse is 9:5, which has been termed the sword verse (ayat al-sayf). It states:
‘And when the sacred months are over, slay the polytheists wherever you find them, and take them captive, and besiege them, and lie in wait for them at every conceivable place.
The first of the sword verses (9:5), with its internal reference to the polytheists who may be fought after the end of the sacred months, would circumscribe its applicability to only the pagan Arabs of Muhammad’s time; this is, in fact, how many medieval scholars, such as al-Shafi’I and al-Tabari, understood the verse. The second of the sword verses is seemingly directed in general at the People of the Book – that is, Jews and Christians – but again, a careful reading of the verse clearly indicates that it does not refer to all the People of the Book, but only those from among them who do not, in contravention of their own laws, believe in God and the Last Day and do not forbid wrongdoing. This understanding is borne out by comparing verse 9:29 to verses 3:113-15, for example, which state:
‘They are not all the same. Among the People of the Book are a contingent who stand [in prayer] reciting the verses of God at all times of the night while they prostrate. These are they who believe in God and the Last day and enjoin what is right and forbid what is wrong. They hasten to [perform] goods and they are among the righteous. And whatever they do of good will not be rejected [by God] and God knows best the God-fearing.’
The Qur’an, in another verse (2:193), makes unambiguously clear that, when hostile behaviour on the part of the foes of Islam ceases, then the reason for engaging them in war also lapses. This verse states:
‘And fight them on until there no chaos (fitna) and religion is only for God, but if they cease, let there be no hostility except to those who practice oppression.’
The Harshness of the two sword verses is thus considerably mitigated, and their general applicability significantly restricted, by juxtaposing with them conciliatory verses, such as the ones cited above, and other such verses. Among other such verses is the one that has been characterized as the peace verse (8:61):
‘If they incline toward peace, incline you toward it, and trust in God. Indeed, He alone is all-hearing, all-knowing.’
‘Slay them wherever you catch them, and turn them out from where they have turned you out; for persecution is worse than slaughter. But if they cease, God is Oft-forgiving, Most Merciful (2:191-192).’
‘God does not forbid you from being kind and equitable to those who have nether make war on you on account of your religion nor driven you from your homes. God loves those who are equitable (60:8).’
These verses make warring against those who oppose the propagation of the message of Islam, and consequently resort to persecution of Muslims, contingent upon their continuing hostility. Should they desist from such hostile persecution and sue for peace instead, the Muslims are commanded to accede to their request. The Qur’an (60:8) further makes clear that non-Muslims of goodwill and peaceableness cannot be the targets of war simply on account of their different religious backgrounds.” 
“As a matter of fact, reading verse 5 of chapter 9 in isolation supports the view that Muslims should fight pagans for their Disbelief, but this same verse must be read together with the proceeding verses of the same chapter. Hence, if we read this verse (9:5) in the light of the following three verses only (9:6,7, and 8) the claim for killing pagans for their paganism becomes void. …” 
We have examined the historical and the scholarly side related to chapter 9 (specifically 9:5), there is one conclusion that can be drawn: Chapter 9, verse 5 was meant to be defensive. In the sense, that it was revealed concerning the pagan Arabs who broke the treaty and fought the Muslims (Khuza’a). Prophet Muhammed (p) did not fight them for their beliefs, rather for breaking the treaty and killing Banu Khuza’a’s people.
As shown, the true Islam, real Islam which was practised by Prophet Muhammed (p) was to repel evil and the brutality of Quraysh.
 Ibn Kathir:
“(then stand you true to them. Verily, Allah loves those who have Taqwa.) The Messenger of Allah and the Muslims preserved the terms of the treaty with the people of Makkah from the month of Dhul-Qa`dah in the sixth year ﴿of Hijrah﴾, until the Quraysh broke it and helped their allies, Banu Bakr, against Khuza`ah, the allies of Allah’s Messenger . Aided by the Quraysh, Banu Bakr killed some of Bani Khuza`ah in the Sacred Area! The Messenger of Allah led an invasion army in the month of Ramadan, of the eighth year, and Allah opened the Sacred Area for him to rule over them, all thanks are due to Allah. …” (Tafsir Ibn Kathir on Surah 9:7, Online Source).
Tafsir Ibn Kathir:
“It was also said that these Ayat refer to the idolators breaking the peace agreement with Muslims and aiding Bani Bakr, their allies, against Khuza`ah, the ally of the Messenger of Allah. This is why the Messenger of Allah marched to Makkah in the year of the victory, thus conquering it…” (Tafsir Ibn Kathir on Surah 9:13, Online Source).
 Tafsir Jalalayn:
(except for those you made a treaty with at the Masjid al-Haram) Referring to the Treaty of Hudaybiyya. They are the Quraysh who were exempted before. (As long as they are straight with you, be straight with them) i.e. as long as they carry out the treaty and do not break it, you should fulfill it. The ma is conditional and not adverbial. (Allah loves those who have taqwa) The Prophet was straight in his treaty with them until they broke it by helping the Banu Bakr against Khuza’a. (9:7). (Tafsir al-Jalalayn on Surah 9:7, Online source)
Tafsir al-Jalalyn 9:13
Will you not (a-la, ‘will not’ or ‘is not’, denotes incitement) fight a people who broke, violated, their oaths, their pacts, and intended to expel the Messenger, from Mecca — for they discussed this between them in their council assembly — initiating, combat, against you first?, when they fought alongside Banu Bakr against Khuza‘a, your allies? So what is stopping you from fighting them? Are you afraid of them? God is more worthy of your fear, when you fail to fight them, if you are believers. (Tafsir al-Jalalayn on Surah 9:13, Online source)
[ As-Sawi: This refers to the Treaty of al-Hudaybiyya which stipulated that there would be no war for twenty years. The Banu Bakr formed an alliance with Quraysh and the Khuza’a with the Prophet. Banu Bakr then attacked Khuza’a and Quraysh helped them with weapons, thus breaking the treaty. ‘Amr b. ‘Allam al-Khuza’i went and informed the Prophet what had happened. The Prophet said, “You will not be helped if I do not help you,” and made preparations and went to Makka and conquered it in 8 AH. In 9 AH, the Prophet wanted to make hajj and he was told that the idolaters were there doing tawaf of the House naked. He said, “I do not want to go on hajj until that no longer takes place. So he sent Abu Bakr that year as amir over the hajj to carry out the hajj for the people. Then he, may Allah bless him and grant him peace, sent Ô Ali to recite these verses on the Day of Sacrifice and to say that after that year, no idolater could make hajj nor do tawaf of the House naked.] (Tafsir as-Sawi on Surah 9:3 – Online source)
 Tanwir al-Miqbas min Tafsir Ibn ‘Abbas:
“(Will ye not fight a folk) why is it that you do not fight a people, i.e. the people of Mecca (who broke their solemn pledges) which are between them and you, (and purposed to drive out the messenger) and wanted to kill the Messenger when they entered Dar al-Nadwah (and did attack you first) by breaking their pledge when they helped the Banu Bakr, their allies, against the Banu Khuza’ah, the allies of the Prophet (pbuh)? (What! Fear ye them?) O believers, do you fear fighting them? (Now Allah hath more right that you should fear Him) because of leaving His command, (if ye are believers).” (Tanwir al-Miqbâs min Tafsir Ibn ‘Abbas on Surah 9:13 – Online Source)
 Tafsir Anwarul Bayan volume 2, page 427
 Islam and International Law: Engaging Self-Centrism from a Plurality of Perspectives, Asma Asfaruddin, volume 7, page 60
 Tafsir Al Qurtubi, Classical Commentary Of The Holy Qur’an, [Dar al-Taqwa], volume 1, page 490 – 491
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought By Asma Afsaruddin, page 88
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought By Asma Afsaruddin, page 88
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought by Asma Afsaruddin, page 89
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought by Asma Afsaruddin, page 89
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought By Asma Afsaruddin, page 89
 Striving in the Path of God: Jihad and Martyrdom in Islamic Thought By Asma Afsaruddin, page 89 – 90
 Guidance To The Uncertain In Reply To The Jews And The Nazarenes (‘Hidayatul Hayara Fi Ajwibatul Yahud wa al-Nasara’) – [Translated by Abdelhay El-Masry, Dar Al-Kotob Al-Ilmiyah] by Imam Ibn Qayyim al-Jawziah, page 25 – 27
 Crescent and Dove: Peace and Conflict Resolution in Islam [United States Institute Of Peace Press Washington, D.C., 2010] by Asma Afsaruddin, page 44 – 47
 Muslims and Non-Muslims : Peace and Convenant , by Mashhad Al-ʻAllaf, page 39 – 40