Some of the Qur’anic verses which lay out the purpose and nature of war include the following:



To stop oppression: “To those against whom war is made, permission is given to fight, because they are oppressed. Verily, God is Capable of aiding them. They are those who have been expelled from their homes in defiance of what is just, for no other reason than that they say, “Our Lord is God.” Had God not restrained one set of people by means of another, monasteries, churches, synagogues, temples and mosques wherein God’s name if oft-mentioned would have been destroyed. God will certainly aid those who aid His cause. (Qur’an, Chapter 22:39-40). Notice the mention of all houses of worship.



In self-defense: “Fight in the cause of God against those who fight you, but do not transgress limits by aggressing; surely God does not love transgressors.” (Qur’an, Chapter 2:190.) Notice that permission is given to fight in self-defense, but not to transgress.



Peace is a desired state: “If they incline toward peace, then seek you peace also. And place your trust in God, for God hears and knows all things.” (Qur’an, Chapter 8:61).

Muslim extremists get their textual interpretations by taking verses in the Qur’an out of their social-historical context, not considering the time, place, and specific circumstances in which these verses were revealed. The commonly quoted verse that follows must be understood in its proper context, namely during the struggle of the early Muslims against the specific group of Makkans who fought, persecuted and killed them first in Makkah, and then after they established a state in Medina, where early Muslims fought back for the first time. These verses can neither be used to justify killing non-Muslims, nor targeting innocent civilians.

”Fight and slay 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 God is Oft-forgiving, Most Merciful. If any among them asks for asylum, grant it to him so that he may hear the word of God. Then escort him to his place of security. This is because they are without knowledge.” 

*Note that even in this social-historical context, not only were the perpetrators given a chance to repent, but that if they sought asylum, it must be granted.