Whenever critics bring verses of the Quran to demonstrate that Islam is violent, that it sanctions Muslims to kill non-Muslims (as claimed by them), they do a cut and paste of a verse and try to hide its context. They don’t show the previous and the verses after, what it actually says. Take for example this passage,
“So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captive 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.” – Quran 9:5
According to some online critics’ they claim, “this verse approves the killing of non-Muslims anywhere at any-time.” This is simply not true. This passage has always been quoted out of context. They never post other verses 9:1-14, for if they did, people would find out that it says the opposite of what they claim. Let’s read from 9:1 – 9:14,
9:1 [This is a declaration of] disassociation, from Allah and His Messenger, to those with whom you had made a treaty among the polytheists.
9:2 So travel freely, [O disbelievers], throughout the land [during] four months but know that you cannot cause failure to Allah and that Allah will disgrace the disbelievers.
9:3 And [it is] an announcement from Allah and His Messenger to the people on the day of the greater pilgrimage that Allah is disassociated from the disbelievers, and [so is] His Messenger. So if you repent, that is best for you; but if you turn away – then know that you will not cause failure to Allah . And give tidings to those who disbelieve of a painful punishment.
9:4 Excepted are those with whom you made a treaty among the polytheists and then they have not been deficient toward you in anything or supported anyone against you; so complete for them their treaty until their term [has ended]. Indeed, Allah loves the righteous [who fear Him].
9:5 And when the sacred months have passed, then kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush. But if they should repent, establish prayer, and give zakah, let them [go] on their way. Indeed, Allah is Forgiving and Merciful.
9:6 And if any one of the polytheists seeks your protection, then grant him protection so that he may hear the words of Allah. Then deliver him to his place of safety. That is because they are a people who do not know.
9:7 How can there be for the polytheists a treaty in the sight of Allah and with His Messenger, except for those with whom you made a treaty at al-Masjid al-Haram? So as long as they are upright toward you, be upright toward them. Indeed, Allah loves the righteous [who fear Him].
9:8 How [can there be a treaty] while, if they gain dominance over you, they do not observe concerning you any pact of kinship or covenant of protection? They satisfy you with their mouths, but their hearts refuse [compliance], and most of them are defiantly disobedient.
9:9 They have exchanged the signs of Allah for a small price and averted [people] from His way. Indeed, it was evil that they were doing.
9:10 They do not observe toward a believer any pact of kinship or covenant of protection. And it is they who are the transgressors.
9:11 But if they repent, establish prayer, and give zakah, then they are your brothers in religion; and We detail the verses for a people who know.
9:12 And if they break their oaths after their treaty and defame your religion, then fight the leaders of disbelief, for indeed, there are no oaths [sacred] to them; [fight them that] they might cease.
9:13 Would you not fight a people who broke their oaths and determined to expel the Messenger, and they had begun the attack upon you the first time? Do you fear them? But Allah has more right that you should fear Him, if you are [truly] believers.
9:14 Fight them; Allah will punish them by your hands and will disgrace them and give you victory over them and satisfy the breasts of a believing people.
When we read from verse 1, it states that there was a treaty which the Pagan Arabs broke. Thus, Allah in the Quran says, that HE gave them four months. Verse 9:4 states that Allah will punish those who broke the treaty. This verse is only aimed at those who broke the treaty, it did not affect those who abided by the treaty. When we read the passage (9:5), it is evident it’s talking about a war with the pagan Arabs. This was a historical event that took place in the lifetime of Prophet Muhammad (p).
Furthermore, verse 9:13 provides proof that it was the pagans who started this war. The verse states, “Would you not fight a people who broke their oaths and determined to expel the Messenger, and they had begun to attack you first?” This is proof that Prophet Muhammad (p) did not start this war, but it was those pagan Arabs that started to expel and fight the Messenger.
For a more up to date and detailed historical analysis on Quran 9:5, please click on the following article: “A Historical Examination Of The Sword Verse – Surah 9:5”
Two non-Muslim translations for Quran 9:13,
John Medows Rodwell What! will ye not fight against those Meccans who have broken their oaths and aimed to expel your Apostle, and attacked you first? Will ye dread them? God is more worthy of your fear, if ye are believers!
N J Dawood Will you not fight against those who have broken their oaths and conspired to banish the Apostle? They were the first to attack you. Do you fear them? Surely God is more deserving of your fear, if you are true believers.
Factors of breakers of the treaty ”Will you not fight people who
A) broke their oaths
B) determined to expel the Messenger
C) attacked you first
Do you fear them? But God has more right that you should fear him, if you are believers Surah 9:13
As it is shown, in that context, those idolaters in Arabia who violated their treaties and attacked the Muslims first, basically, the Muslims were allowed to fight back in self-defence. Why is it that critics never show 9:6? Let’s read:
9:6 And if any one of the polytheists seeks your protection, then grant him protection so that he may hear the words of Allah. Then deliver him to his place of safety. That is because they are a people who do not know.
The verse shows that if any of the idolaters who broke the treaty, and wanted protection, that they should granted protection and that they deliver him/her to a ‘place of safety’. This shows even when they who broke the treaty – when they attacked the Muslims first, the Muslims were commanded by Allah to make peace if they asked. Hence, it’s evident reading the verses in its context that this was a war of self-defence against the pagan Arabs who broke the treaty and attacked the Muslims.
Commentary on 9:5 by Muslim and non-Muslim scholars
Ustadh Faraz A. Khan commenting on Quran 9:5 says,
Context of the Verse of the Sword [9:5]
…….the Verse of the Sword deals specifically with the situation of Meccan polytheists breaking peace treaties and openly declaring war on the Muslim polity. The verse, then, commands the Muslim state to take up arms and defend itself against those that breached their covenants and attacked out of treachery.
This explanation is confirmed by the most reliable Imams of Qur’anic exegesis [tafsir], including Imam Razi, Imam Jamal, Imam Zamakhshari, Imam Baydawi, Imam Nasafi, Imam Biqa`i, and others.
[Razi, Mafatih al-Ghayb; Jamal, Hashiyat al-Jalalayn; Zamakhshari, Kashshaf; Baydawi, Anwar al-Tanzil; Nasafi, Madarik al-Tanzil; Biqa`i, Nadhm al-Durar]
The verse, therefore, can by no means be generalized to refer to all disbelievers. Such an interpretation is not confirmed by scholars of Qur’anic interpretation. It would be both contrary to the intent of the verses as well as disastrous for the security of both Muslim and non-Muslim citizens and nation-states. 
Islamic Scholar Muhammad Asad commentary
“5 Lit., ‘Until their term’.
6 According to a pre-Islamic custom prevalent in Arabia, the months of Muharram, Rajab, Dh’l-Qa’dah and Dhu’l-Hijjah were considered ‘sacred’ in the sense that all tribal warfare had to cease during those months. It was with a view to preserving these periods of truce and thus to promoting peace among the frequently warring tribes that the Qur’an did not revoke, but rather confirmed, this ancient custom. See also 2:194 and 217
7 Read in conjunction with the preceding verses, as well as with 2:190-194, the above verse relates to warfare already in progress with people who have become guilty obligations and of aggression.
8 I.e., ‘do everything that may be necessary and advisable in warfare’. The term marsad denotes ‘any place from which it is possible to perceive the enemy and to observe his movements (Manar x, 199). 9 As I have pointed out on more than one occasion, every verse of the Qur’an must be read and interpreted against the background of the Qur’an as a whole.
The above verse, which speaks of a possible conversion to Islam on the part of ‘those who ascribe divinity to aught beside God’ with whom the believers are at war, must, therefore, be considered in conjunction with several fundamental Qur’anic ordinances. One of them, ‘There shall be no coercion in matters of faith’
(2:256), lays down categorically that any attempt at a forcible conversion of unbelievers is prohibited-which precludes the possibility of the Muslims demanding or expecting that a defeated enemy should embrace Islam as the price of immunity.
Secondly, Qur’an ordains ‘Fight in God’s cause against those who wage war against you; but do not commit aggression, for, verily, God does not love aggressors’ (2:190); and, ‘if they do not let you be, and do not offer you peace, and do not stay their hands, seize them and slay them whenever you come upon them: and it is against these that we have clearly empowered you [to make war]’ (4:91).
Thus, war is permissible only in self-defence (see surah 2, notes 167 and 168, with the further proviso that ’if they desist- behold, God, God is much-forgiving, a dispenser of grace’ (2:192), and ‘if they desist, then all hostility shall cease’ (2:193). Now the enemy’s conversion to Islam- expressed in the words,
‘if they repent, and take to prayer [lit., ‘establish prayer’] and render the purifying dues [zakah]’- is no more than one, and by no means the only, way of their ‘desisting from hostility’; and the reference to it in verses 5 and 11 of this surah certainly does not imply an alternative of ‘conversion or death’, as some unfriendly critics of Islam choose to assume. Verse 4 and 6 give a further elucidation of the attitude which the believers are enjoined to adopt towards such of the unbelievers are not hostile to them. (In this connection, see also 60:8-9).” 
In the Book ‘Understanding the Qur’an Themes and Style’, Dr. Muhammad Abdel Haleem writes:
“We must also comment on another verse much referred to but notoriously misinterpreted and taken out of context – that which became labelled as the ‘Sword verse’ : “…Then when the sacred months have passed, slay the idolaters wherever you find them, take them and besiege them and prepare for them every ambush….” [ 9:5 ]
The hostility and “bitter enmity” of the polytheists and their fitna [ persecution, 2:193 ; 8:39 ] of the Muslims grew so great that the unbelievers were determined to convert the Muslims back to paganism or finish them off. “…They would persist in fighting you until they turn you back from your religion, if they could….” [ 2:217 ]
It was these hardened polytheists in Arabia, who would accept nothing other than the expulsion of the Muslims or their reversion to paganism, and who repeatedly broke their treaties, that the Muslims were ordered to treat in the same way – to fight them or expel them….Even with such an enemy Muslims were not simply ordered to pounce on them and reciprocate by breaking the treaty themselves; instead, an ultimatum was issued, giving the enemy notice, that after the four sacred months mentioned in 9:5 above, the Muslims would wage war on them.
The main clause of the sentence “kill the polytheists” is singled out by some Western scholars to represent the Islamic attitude to war; even some Muslims take this view and allege that this verse abrogated other verses on war. This is pure fantasy, isolating and decontextualizing a small part of a sentence.
The full picture is given in 9:1-15, which gives many reasons for the order to fight the polytheists. They continuously broke their agreements and aided others against the Muslims, they started hostilities against the Muslims, barred others from becoming Muslims, “expelled” Muslims from the Holy Mosque and even from their own homes. At least eight times the passage mentions their misdeeds against the Muslims.
Consistent with restrictions on war elsewhere in the Qur’an, the immediate context of this “Sword Verse” exempts such polytheists who do not break their agreements and who keep the peace with the Muslims [9:7], it orders that those enemies seeking safe conduct should be protected and delivered to the place of safety they seek [9:6].
The whole of this context to v. 5, with all its restrictions, is ignored by those who simply isolate one part of a sentence to build their theory of war in Islam on what is termed “The Sword Verse” even when the word sword does not occur anywhere in the Qur’an.” 
Professor Jamal A. Badawi
Common Questions and Objections
1. How do you explain verses in the Qur’an that encourage killing non-Muslims wherever they are found (9:5) and others that allow fighting against Jews, Christians, and other neighboring non-Muslims (9:29, 123)?
Answer: To begin with, the verse (9:5) has nothing to do with the People of the Book (Jews and Christians), who are distinguished from other non-Muslims. The Qur’anic text (98:1) makes a clear distinction between the People of the Book or Ahl Al-Kitab and the idolatrous people, al-mushrikeen, the term used in 9:5.
Furthermore, all these and similar verses have been sometimes misconstrued and taken out of their textual and historical context. They have been taken out of their textual context by ignoring the verses before and after the quoted ones, as well as ignoring other verses in the Qur’an which relate to the same issues and thus shed light on their true meanings. They have also been taken out of the historical context that could explain why they were revealed and how they should be applied.
All of these verses, without exception, if studied carefully, address aggression and oppression committed against Muslims at the time of the Prophet (peace and blessings be upon him), whether by idolatrous Arabs, some of the Jewish tribes in Madinah, or by some Christians. Most, however, apply to the Makkans and other idolatrous Arabs aggressors.
Some of the antagonists tortured, and in certain cases killed, Muslims because of their faith, for example the killing of Sumayyah and her husband Yasir. Some killed the memorizers of the Qur’an who were simply on their way to preach its message of Allah’s Oneness in a peaceful manner.
Some of them killed the messengers sent by the Prophet (peace and blessings be upon him), which is equivalent in today’s international law to killing the ambassador of another country—an act of war. Some of them gathered armies, like the Christians in Tabuk, in order to attack Muslims. Some of them wrote letters to their local governors to go and kill the Prophet Muhammad (peace and blessings be upon him) unless he recanted his claim of prophethood, as was the case with the Emperor of Persia.
Some betrayed peace treaties and killed unsuspecting peaceful people without provocation, contrary to agreements, such as the breaking of the Treaty of Hudaybiah by the Makkans. The issue here is not religion, but rather injustice, oppression, and aggression.
• There are many verses in the Qur’an stating that those who coexist peacefully with Muslims are entitled to justice, compassion, and respect, irrespective of their religion (60:8-9) as long as they are peaceful with Muslims.
• If it were true that the Qur’an instructs that any non-Muslim should be killed because of his or her religion, then what would explain the fact that religious minorities through 1,400 years of Muslim history not only survived, but also thrived and found freedom to practice their faiths under Muslim rule?
Clearly, Muslims as a people were not perfect, yet there were times when they had enough power to eliminate almost all non-Muslims under their rule. The historical record shows that they did not abuse this power. The restraint they showed seems to be influenced in the first place by the Qur’anic injunctions against coercion in religion.
• The Qur’an allows a Muslim man to get married to a Christian or Jewish woman. If it were true that the Qur’an demands killing non-Muslims, how could it permit a Muslim man to marry such women? Marriage is the closest human relationship and is described in the Qur’an as a relationship characterized by peace, love, and compassion (30:21), not murder because of theological differences. 
Commentary on the Holy Quran By Zohurul Hoque and Husein Nuri
9:5 Regarding the significance of sacred months see notes to v. 2. Many malicious critics of Islam fully exploited the outward message of the verse to project a seriously distorted picture of Islam and concluded its militant stance is the cause behind many of the hostilities in the world. Their basic analogy is how this religion, bearing a name of peace, could teach killing innocent people.
The critics try to portray every Muslim is required to slay every non-Muslim wherever they may find them, at peace time or otherwise. In this context, it is important to note that nowhere in the Qur’ān, free permission was given to kill anyone anywhere. Therefore, the message of the verse must be objectively analyzed and interpreted in context of the revelation and its application must be done in circumstances similar to that necessitated the revelation.
Regardless of the name or intent of the religion, the Qur’ān, being a complete guide for every problem at personal, communal and state level, must address what should be done if fundamental rights of a community or a nation are violated due to armed aggression and appropriate collective redress cannot be established due to lack of a system to assure peace or disinterest and/or inability of a system to solve the crisis.
With or without the Qur’ānic instruction, a Muslim community or a nation is expected to react exactly the same way a non-Muslim community or a nation would react if they are attacked or war is waged against them. Only difference is a non-Muslim community or a nation would defend itself against hostile aggression or war out of their instinctive or constitutional right to protect them, without having to recourse to their scriptures.
Since no other scripture claims to contain ‘complete guidance’ for mankind, it is no surprise to see they do not address complex socio-political issues of war and peace. Before giving the permission to capture, wait in ambush or slay the unbelievers, the Qur’ān made it clear to comply with peace treaty with those who are willing to uphold it (previous verse).
It must be remembered that initiative for all peace treaty was made from the Muslim side, as war was not seen as an objective of Islam. It must also be remembered that in the pre-Islamic era and during the development of Islamic era, annulment of peace treaty between two hostile tribes was nothing but declaration of open war.
The Muslims were therefore, specifically instructed to fight against those tribes that annulled peace treaty. In this regard, specific notation of 2:190-193 may be made that say: and fight in the way of Allāh against those who fight with you and do not transgress. Thus, war is permissible only in self-defense, and not as an act of active aggression. While in a war Islam permits everything necessary and advisable in warfare, yet it prohibits undue aggression in war (2:190, 193; 8:39,61-62).
The malicious critics of Islam often quote the second half of the verse to imply that non-Muslims were converted into Islam with great degree of coercion. This message must be reviewed in conjunction with several other fundamental ordinances of the Qur’ān that say: there is no compulsion in religion, the Right Path has indeed been made distinct from the wrong (2:256; also see 6:105; 10:99; 18:29; 27:92; 42:15; 73:19; 76:29).
Keeping this in mind, the only way the captives in war could be prevented from reverting to hostility upon their release was to make them embrace Islam. Such conversion in Islam was purely as a war strategy and should not be viewed as general approach during peacetime or as intolerance of their faith. In every age, the hostile pastors of many Churches quoted this ruling of the verse in a much generalized sense to incite hatred towards Islam.
Nowhere the verse says the captives were to be converted. Three things about the captives are stated: (a) if they repent, (b) if they keep up salāt, and (c) if they pay zakat, they should be left alone on their path. The condition of professing faith in Islam is clearly absent. Mention of salāt and zakat may have misled the critics into believing the captives were converted into Islam and then left alone.
Even before the advent of Islam, the Arabs were accustomed to performing salāt and paying zakat, just as Ibrāhīm, Ismā‘īl, Mūsā, Jesus and their disciples were mandated to perform salāt and pay zakat (19:31,55; 21:73). By sincerely expressing repentance for waging war and then by showing adherence to their form of salāt and zakat, the captives would have rightly demonstrated change in their evil intentions. 
The Holy Quran Arabic Text with English Translation, Commentary and comprehensive Introduction, Maulana Muhammad Ali
4a. Only two tribes, the Bani Damarah, and the Bani Kananah, are related to have adhered to their treaties. The exception given here makes it clear that the Muslims were not fighting with the idolaters on account of their religion, but on account of their having been untrue to their engagements.
5a. The clear exception of the last verse shows that by the idolaters here are meant, not all idolaters or polytheists wherever they may be found in the world, not even all idolaters of Arabia, but only those idolaters tribes of Arabia assembled at the pilgrimage who had first made agreements with the Muslims and then violated them.
5b. The exception here has given rise to much misconception. It is thought that it offers to the disbelievers the alternative of the sword or the Qur’an. Nothing is farther from the truth.
The injunction contained in the first part of the verse establishes the fact that the whole verse relates to certain idolatrous Arab tribes who had broken their engagements with the Muslims, and who had now been apprised of a similar repudiation by the Muslims.
The order to kill them and to make them prisoners and to besiege them and ambush them amounts clearly to an order to fight against them, as it is in war only that all these things are made lawful. They had so often broken their word that they could no more be trusted. Yet, if they joined the brotherhood of Islam, and there was an absolute change in their condition, the punishment which they otherwise deserved could be remitted.
It was a case of forgiving a guilty people who had repented. It should also be noted that a mere confession of the faith is not required; what is required is an absolute change, so that the old crimes are all abandoned. Therefore, along with the confession of the faith, it Is required that they should keep up the prayer and pay the poor-rate. The subject is further clarified in the next verse and the following section.
6a. This verse leaves no doubt that the Prophet was never ordered to kill anyone one account of his religion. “You shall give a safe-conduct that he may return home again securely in case he shall not think fit to embrace Islam” (Sale).
7a. So long as the idolaters were true to their agreements, the Muslims were required to be true to them. Just as in the case of war, the Muslims were not allowed to fight until the enemy had first attacked, so, in the case of repudiation of agreements, it was the enemy who first repudiated the agreement.
10a. Note the repeated assertions of the Qur’an that the disbelievers were not to be fought against for their disbelief but for their being first in starting war or repudiation agreements. No remedy was left for the covert mischief if these people, except that the agreements should be overtly repudiated and a period put to all their mischief. 
The Holy Qur’an Arabic Text with English Translation and short Commentary, Malik Ghulam Farid
1155A. ‘The forbidden months’ are the four months of Dhu’l-Qa’dah, Dhu’l-Hijjah, Muharram and Rajab, the first three being the months of the Greater Pilgrimage, while in the last the Arabs generally performed the lesser pilgrimage or ‘Ummah (2:195 & 2:218).
The term Ashur Al-Hurum does not signify ‘sacred months’ but ‘forbidden months’ and refers to the four months mentioned in 9:2 above. In these months the above-mentioned idolaters were granted protection to travel through the land and see for themselves whether Islam had not triumphed and whether the word of God had not been fulfilled.
At the end of this period, during which all hostilities were to remain suspended, war was resumed against such avowed enemies of Islam as had themselves started hostilities and had repeatedly broken their plighted word. The reason for this ultimatum is given in vv. 9:8-13. As for those idolaters who had not been guilty of faithlessness and treachery, they were to be protected (9:4, 7).
1156. Those idolaters who had fought with the Muslims and not yet asked for a fresh treaty with them.
1157. Even those enemies of Islam at whose hands Muslims had suffered very grievous losses were to be forgiven if they repented and accepted Islam of their own free will. In fact, there was a large number of men among the idolaters who, in their heart of hearts, had been convinced of Islam, but who, either pride or fear of persecution or other considerations, had refrained from open confession of faith.
This verse assured such people that if anyone of them declared his faith in Islam even during the war, his confession would not be taken as hypocritical or as having been to save his skin.
1158. The verse clearly establishes the fact that war with idolaters was not undertaken in order to force them to embrace Islam, because, according to it, even when a state of war existed, idolaters were to be permitted to come to the Muslims’ camp or headquarters if they desired to investigate the truth.
Then, after the truth had been preached to them and they had been acquainted with the teachings of Islam, they were to be safely conducted to their place of security, if they did not feel inclined to embrace to the new faith. In the face of such clear teachings, it is the height of injustice to accuse Islam of intolerance or o using or conniving at force; for its propagation.
1159. The verse shows that war was permissible only against such non-Muslims as had repeatedly violated most solemn covenants and had attacked Muslims treacherously. As for the rest, Muslims had been bidden to observe their engagements with them strictly and faithfully. Like 9:4, this verse describes the observance of covenants and treaties as an act of piety and righteousness which is pleasing to God. The Qur’an repeatedly and most emphatically exhorts Muslims to be faithful to their treaties.
Professor David Dakake Islamic Research Institute Washington, D.C says:
Another verse which has caused much confusion is 9:5. This is the first Quranic verse mentioned in the fatwa of Usama bin Ladin. It is also a verse which has been referred to by Reverend Franklin Graham in his comments about the “wicked, violent” nature of Islam. Verse 9:5 says,
But when the forbidden months are past, then fight and slay the polytheists (mushrikun) wherever you find them, seize them, beleaguer them, and lie in wait for them in every strategem [of war]. Contrary to what may be thought from a literal reading of this translation, this verse is not a kind of carte blanche to attack any and all non-Muslim peoples. Here again the issue of historical context is so crucial for understanding.
Verse 9:5 was revealed specifically in relation to the Muslims fighting the idolaters of Makkah. The Makkan idolaters are referred to in the Quran by the technical term “mushrikun” (sing. “mushrik”). This term comes from a three letter Arabic root “sh-r-k” which means “to associate” or “take a partner unto something,” so that the word mushrikun literally means, “those who take a partner [unto God],” that is to say, “polytheists” or “idolaters.”
It should be noted, therefore, that the injunction in this verse to fight against the “polytheists” does not pertain to either Jews or Christians from the point of view of Islamic Law. Interestingly, Jews and Christians are never referred to within the Quran by the term mushrikun.
They have, in fact, a very different “status” or “title” according to the Quran which, when not addressing them as individual communities, often refers to the two groups together by the technical term, ahl al-kitab or “People of the Book,” meaning people who have been given a book or scripture by God other than the Muslims.
Given these facts, it is interesting that this verse should be cited by Bin Ladin in the context of a declaration calling on Muslims to fight Jews and Christians, particularly since this verse says nothing about Jews, Christians or the People of the Book in general. This being the case, the fatwa’s use of 9:5 represents a misappropriation of this verse to an end other than the one intended from its established historical context of fighting the “polytheist” Arabs, who were neither Christians nor Jews.
Given this context, this verse does not, in fact, show Islam to be a “wicked, violent” religion, as Franklin Graham would like us to believe, but shows that Islam gave to Muslims the right to defend themselves against those who would not let them worship God, a right, incidentally, which is protected by the United States Constitution. 
John Louis Esposito is an American professor of International Affairs and Islamic Studies at Georgetown University in Washington, D.C., he writes:
Permission to fight the enemy is balanced by a strong mandate for making peace: ‘If your enemy inclines toward peace, then you too should seek peace and put your trust in God’ (8:61) and ‘Ha Allah wished, He would have made them dominate you, and so if they leave you alone and do not fight you, and offer you peace, then Allah allows you no way against them’ (4:90).
From the earliest times, it was forbidden in Islam to kill non-combatant as well as women and children and monks and Rabbis, who were given the promise of immunity unless they took part in the fighting.
But what of those verses, sometimes referred to as the ‘sword verses,’ that call for the killing unbelievers, such as, ‘When the sacred Months have passed, slay the idolaters wherever you find them, and take them, and confine them, and lie in wait for them at every place of ambush’ (9:5)? This is one of a number of Quranic verses that are cited by critics to demonstrate the inherently violent nature of Islam and its scripture.
These same verses have also been selectively used (or abused) by religious extremists to develop a theology of hate and intolerance and to legitimate unconditional warfare against unbelievers….. the full intent of ‘When the sacred months have passed, slay the idolaters wherever you find them’ is missed or distorted when quoted in isolation.
For it is followed and qualified by: ‘But if they repent and fulfil their devotional obligations and pay the zakat, then let them go their way, for God is forgiving and kind’ (9:5). The same is true of another often quoted verse: ‘Fight those who believe not in God nor the Last Day, nor hold that forbidden which hath been forbidden by God and His Apostle, nor hold the religion of truth [even if they are] of the people of the Book,’ which is often cited without the line that follows, ‘Until they pay the tax with willing submission, and feel themselves subdued’ (9:29).
Throughout history, the sacred scriptures of Judaism, Christianity, and Islam have been used and abused, interpreted and misinterpreted, to justify resistance and liberation struggles, extremism and terrorism, holy and unholy wars. Terrorists like Osama Bin laden and others go beyond classical Islam’s criteria for a just Jihad and recognize no limits but their own, employing any weapons or means.
They reject Islamic law’s regulations regarding the goals and legitimate means for a valid Jihad: that violence must be proportional and that only necessary amount of force should be used to repel the enemy, that innocent civilians should not be targeted, and that Jihad must be declared by the ruler or the head of state. Today, individuals and groups, religious and lay, seize the right to declare and legitimate unholy wars of terrorism in the name of Islam. 
Dr. Zakaria Bashier
This is the verse of the sword indeed, but its military is in response to that of the idolaters of the Quraysh. It was the Quraysh who persecuted Prophet Muhammed (p), and his followers in Makkah and eventually forced them to leave the Holy City of their homeland, leaving behind their wealth and property.
But even here, the way in which this verse finishes off, advocates tolerance and forgiveness, should those polytheists of the Quraysh change their way, and repent their former insolence. If they intended their peaceful intentions, their desire to take refuge in the camp of the Muslims or their desire to listen to the Qur’an, then they should be allowed to go freely, says God in the immediate next verse:
If one of the idolaters ask you for asylum, grant it to him; so that he may hear the word of God, then escort him to where he can be safe and secur, that is because they are men without knowledge’. [Al-Tawbah 9:6]
As we said before, this verse expresses the peacefulness of Islam and the prophet’s basic desire for peace; that peace is the rule, hostilities are the exception, even with former belligerents and enemies such as the Qurayshites, peaceful coexistence is preferable, should they be willing. The idea is that and enemy may fight the Muslims out of ignorance and hatred … Therefore every chance for peace and reconciliation must be seized to educate him, and remove the subjective factors of hate and prejudice.
Immediately following these verses (7 and 8 Surah al-Tawbah), verses which advocate war against the Qurayshite idolaters. It says that Qurayshite Idolaters have no respect for their covenants or pledges which they made to the Muslims.
They were the ones that started aggression and hostilities, and should they prevail over the Muslims, they would destroy them, heeding neither the bonds of family, nor any pledges or covenants they made with them. That the advocacy of hostilities against the Quraysh idolaters was a special case, governed by specific circumstances, and historical relations between the Muslims and those idolaters. So any attempt to generalize from that or infer from it that Islam is a violent religion does not hold. 
As we have examined the passage, which is often quoted by critics that Islam sanctions the killing of non-Muslims, it turns that this not true. When the context of the passage is shown, we see that this verse was revealed in order to fight the Pagan Arabs at the time of the Prophet Muhammed (p). The pagans Arabs were the ones who expelled the Prophet, broken the treaty and also started fighting the Muslims.
What were the Muslims supposed to do? Of-course the Prophet (p) had to fight back in self-defence in order to defend the Muslim community from being massacred by those treacherous pagan Arabs. I also provided many Muslim and non-Muslim scholarly views on the passage (9:5), and they all unanimously agree that this war was a war of self-defence, against the Pagan idolaters who broke the treaty, and started attacking the Muslims first.
 Ustadh Faraz A. Khan http://seekersguidance.org/ans-blog/2010/11/06/jihad-abrogation-in-the-quran-the-verse-of-the-sword/
 The Message of The Quran translated and explained by Muhammad Asad http://www.usc.edu/schools/college/crcc/private/cmje/religious_text/The_Message_of_The_Quran__by_Muhammad_Asad.pdf
 Understanding the Qur’an Themes and Style by Muhammad Abdel Haleem page 65 – 66
 Muslim and Non-Muslim Relations Reflections on Some Qur’anic Texts by Dr. Jamal Badawi, PhD April, 05, 2005 http://www.islamawareness.net/MusChristRelations/reflections.html
 Commentary on the Holy Quran By Zohurul Hoque and Husein Nuri http://www.qurancommentary.com/comm9_5.html
 The Holy Quran Arabic Text with English Translation, Commentary and comprehensive Introduction by Maulana Muhammad Ali page 398 – 399
 The Holy Qur’an Arabic Text with English Translation and short Commentary by Malik Ghulam Farid page 377 – 378
 Professor David Dakake Islamic Research Institute Washington, D.C
 What Everyone Needs to Know about Islam, Answers to frequently asked Questions, from one of America’s leading experts [Copyright 2002] by John L. Esposito page 120 – 122
 War and Peace In the Life of the Prophet Muhammed, by Zakaria Bashier page 284 – 285
About Zakaria Bashier (b.1940). He obtained his BA and M.litt. in Philosophy from the Universities of Khartoum, Sudan and Durham, UK respectively, and his PhD on Islamic Philosophy from the University of Pittsburgh, USA. Apart from holding faculty positions at the Universities of Sudan, Saudi Arabia, UAE, he had also been the Vice Chancellor of the University of Juba, Sudan.