Quran:
Chapter 9 verse 5
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). But if they repent and establish regular prayers and practice regular charity, then open the way for them, for Allah is oft-forgiving, most merciful.”
Some people – especially some contemporary non-Muslim critics of Islam – have tried to claim that this verse abrogates the verse “Let there be no compulsion in religion.” They argue that the generality of this statement implies that every unbeliever who refuses to accept Islam must be fought. They support their allegation by pointing out that this verse is one of the last verses to be revealed about fighting.
However, this verse in no way abrogates the principle in Islamic Law that there is no compulsion in religion. It may be general in wording, but its meaning is quite specific on account of other verses of the Quran that are connected with it as well as on account of a number of pertinent hadîth. We will be discussing these texts shortly.
The people being referred to by this verse are the pagan Arabs who had been waging war against the Prophet (peace be upon him) and who had broken their covenant and treaties with him. This verse is not speaking about the other pagan Arabs who did not break their treaties and take up arms against the Muslims. It is also most definitely not speaking about the Jews or Christians, or, for that matter, the pagans who were living outside of Arabia.
If we look at the verses in Surah al-Tawbah( Chap 9) 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.” [Surah 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.” [Surah al-Tawbah: 9:4]
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 by 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?” [Surah al-Tawbah: 9:13]
Ibn al-Arabi, in his commentary on the Quran, 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-Quran: (2/456)]
Allah also say right after the verse under discussion: “How can there be a covenant before Allah and His Messenger with the pagans except those with whom you have made a treaty near the Sacred Mosque? As long as they stand true to you, stand true to them, for Allah does love the righteous.” [Surah al-Tawbah: 9:7]
http://islamtomorrow.com/kill.asp
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