There is also war or combat (qital) in the Qur’an. Whereas jihad is an affirmative duty to confront falsehood with the truth of God, the verses that command war in the Qur’an apply to situations in which a Muslim is called to respond to aggression. In such situations God describes what Muslims may be allowed to do for their own self defense. For instance, if Muslims come under attack; if, their lives, possessions and honor are threatened, if they are being killed and if there is no alternative but to fight, then it becomes obligatory and lawful for Muslims to defend themselves and to come to the aid of the innocent.
Pagan rule and self defense – In order to understand the Qur’anic prescriptions to war, it is necessary to understand the historical context in which the commandments came. The revelation of the Qur’an to Prophet Mohammad was delivered over a period of 23 years. The first thirteen years of this period passed in Mecca, where Muslims lived as a minority and faced much oppression under a pagan rule. At that time, the Arabian peninsula was dominated by Bedouin Arab tribes who wandered about looting, robbing and murdering as a manner of life. They were hooligans that murdered, got drunk and enjoyed killing people. They made war against the Prophet Mohammad and against anyone who followed his teachings. When they were warned not to murder, they kept on murdering. Despite the fact that many Muslims were harassed, dispossessed of their homes, abused, tortured, and even murdered, Muslims strove to co-exist without resorting to any violence and always called pagans to peace. As a matter of fact, the Muslims dug trenches in the Khandaq war as a defensive strategy to avoid conflict as much as possible. They also emigrated (hejira), and ran away from them, but even then the aggressors pursued them.
In sum, nowhere in the Qur’an are Muslims commanded to wage wars of aggression, and certainly not as a means for to propagate Islam. If a community does not attack, and behaves normally, then naturally, there is no call to war. The obligation to war is and remains a limited, unwanted obligation, applicable only to repel attack.
War commandments – It is not an easy thing to decide to wage war, and Prophet Mohammad was undecided, worrying about whether he would be committing a sin. As the aggressors in question are human beings, he felt a responsibility of conscience and was unable to make a decision. Under these circumstances, God commanded the Prophet Mohammad to kill the polytheists wherever he finds them. However that is a commandment delivered within a context of an ongoing war, not as a method for the propagation of Islam. God commanded: “… Whenever they are made to revert to hostility, they fall headlong into it. Therefore, if they do not keep aloof from you, nor offer you peace nor restrain their hands, then seize them and kill them, wherever you find them. Against these We have given you clear authority.” (Qur’an, 4:91)
In this same vein, the Qur’an commands blockade and taking prisoners as a peaceful means of neutralizing a potentially aggressive community (Quran, 9:5). But if a blockade or taking prisoners are not possible, then killing is permissible only as a last resort.
Verses special for a particular time – In addition, some of the verses that are in regard to the strategic wars are specific to that particular period. There is clearly no such situation at the moment. For instance God informs “if they do not accept conditions of agreement”, that refers to a special circumstance. Regarding a battle, God says, “Behold! they came on you from above you and from below you,” (Qur’an, 33:10) and describes a a particular situation. Additionally, there are verses that refer to Prophet Mohammad in particular, and verses specific to a particular event. However a Muslim reads with wisdom and takes lessons from whatever is described in the Qur’an, just like a Jew would read the battles in the Torah with meditation.
Commandments for specific situations and general situations are different. The general commands are orders that are valid until the Day of Reckoning. For instance, God informs us to say, “Your religion is to you, our religion is to us.” (Qur’an, 109:6) This is a general verse. In another verse He says “There is no compulsion in religion,” (Qur’an, 2:256); this is also a general verse. And there certainly is no meaning such as to kill disbelievers or people from other religions, God forbid. It is required that a clear and general command should exist in the Qur’an, but there is no such verse or no general command that is still binding to this day.