Another “sword” verse, Take them and slay them wherever you come on them, is part of an injunction revealed at a time when Muslims were being persecuted in Arabia:

If they leave you alone and do not fight you and offer you peace, then Allah allows you no way against them. [But] if they withdraw not from you nor offer you peace, then take them and slay them wherever you come on them (4:90).

Another oft-cited verse, Fight the leaders of unbelief, has a preceding qualifier, so that the full line reads:

If they break their pledges after their covenant and assail your religion, then fight the leaders of unbelief (9:12).

Similarly, when critics trot out the line, Leave is given to those who fight, they rarely quote the entire injunction:

Leave is given to those who fight, because they have been wronged...[and] expelled from their homes unjustly only for saying, “Our Lord is God.”

Had it not been for God repelling some men by means of others, cloisters, churches, oratories and mosques, wherein God’s name is oft mentioned, would surely have been pulled down (22:39-40).

There are two elements here — one of defensive jihad to counter the religious persecution that Muhammad and his followers were then facing, and the other of concern for the religious freedom of all believers, not just Muslims.

As for the Prophet being a warrior, the concept is not unique to Islam. What of Joshua, David and Solomon? Plus, Muhammad “only fought those who fought him, and his fighting had no other aims than repelling repression, warding off rebellion and aggression, and putting an end to persecution due to religion,” wrote the late Mahmud Shaltut, a former rector of the famed Al-Azhar Islamic academy in Cairo.3

Islamic tradition holds that the verses relating to wars and fighting were overtaken by those revealed during the peace that followed between Muslims and non-Muslims. Hence the later exhortations to avoid war altogether, limit warfare, honor treaties and, if attacked, to respond only proportionately, to protect civilian non-combatants and not mutilate the dead:

Fight them [only] until there is no persecution (8:39).

If your enemy inclines toward peace, then you, too, should seek peace and put your trust in God (8:61).

Warfare is an awesome evil (2:217).

The overall Qur’anic message is clear, said Shaltut: “There are only three reasons for fighting: repelling aggression, protecting Islam and defending religious freedom.”4

Can Muslims undertake a jihad to spread Islam by killing infidels? Arguments on this flow from this Qur’anic line:

When the sacred months have passed, slay the idolaters wherever you find them, and take them and confine them, and prepare to ambush them (9:5).

However, this, too, is qualified by what follows:

But if they repent and establish worship and pay the zakat [charity], then let them go their way, for God is forgiving and kind (9:5).