First references to the subject come from the early times of the Prophet, spent in Mecca. The verses encouraging to conquest and war against unbelievers, however, prevail mostly in the later parts of Quaran .
Surah 8, verse 17 directly says that killing opponents of Islam is God’s decision. Islamic fighters are only tools in the hands of Allah.
‘And you did not kill them, but it was Allah who killed them. And you threw not, [O Muhammad], when you threw, but it was Allah who threw that He might test the believers with a good test.’
– these were the words of Muhammad after the victorious battle of Badr . It was a different line, (Surah II, verse 191), that became a justification of various atrocities in the name of religion:
And kill them wherever you find them and expel them from wherever they have expelled you, and fitnah [Persecution] is worse than killing. And do not fight them at al-Masjid al- Haram until they fight you there. But if they fight you, then kill them. Such is the recompense of the disbelievers. (Surah II, verse 191)
We can find many verses with similar meaning. An expert in the field of Holy War Krzysztof Kościelniak lists 15 of those. Three are of particular interest, as they not only mention victory over unbelievers but also sanction cruelty towards those rejecting Islam:
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.(IX, 5).
Out of this citation clearly stems that Muslims can use any means necessary in the fight against unbelievers, also the cruel ones. Another verse, in the opinion of many Islam interpreters  justifies even the fight in holy places, where, according to a pre-Islamic Arabic custom, conducting wars was forbidden.
Indeed, the number of months with Allah is twelve [lunar] months in the register of Allah [from] the day He created the heavens and the earth; of these, four are sacred. That is the correct religion, so do not wrong yourselves during them. And fight against the disbelievers collectively as they fight against you collectively. And know that Allah is with the righteous [who fear Him]. (IX, 36).
This example shows that Muhammed’s message turned against remaining pacyfist traditions. Many traditional cultures, including the Greeks, had periods, when any wars were forbidden, and anybody, who violated such a ban would be ostracised.
Those defending the peaceful character of Quran often reach to the verse forbidding Muslims leading offensive wars: ‘Fight in the way of Allah those who fight you but do not transgress. Indeed. Allah does not like transgressors.’ (II, 190).
However, it has be said, that if Muslims had obeyed by that verse, they would be a local sect today, as the developement of Islam in almost all the cases was due to conquest. This verse was not practiced by neither Muhammad himself, nor his followers. Additionally, the theological tradition and actions of Muslims over centuries stand in complete contradiction to it. Experts draw our attention to this fact by writing:
‘Calls like “do not be transgressors” resemble the medieval righteous war theory. Everything would be alright, had the first Muslims abode by that rule. Meanwhile, if we look closely at Surah II, 190-191, we will see clearly, that it is indeed an accusation against Muslims themselves for conquest of Christian countries. When Islam believers raided and looted Syria and Egypt in 636-641, they did it as transgressors indeed. Over time within the Muslim theology a theory has developed, that any truce can be broken one-sidedly, if beneficial for Islam. Legal distincition of different categories of the conquered land and conquest propaganda developed with the expansion of Islam, then the meaning of Surah II, 190 ‘but do not transgress’ was not taken into account’.
The issue of that verse reveals an important characteristics of Islam, that is the acceptance of immoral behaviour, if it is to strenghten its position. Here we can see a clear difference between ancient Greek philosophy, Christian ethics, Roman law and the Muslim culture. The European culture sees abiding own rules as a virtue. Sokrates chose death above denying his ideals. Jesus thought compassion and openly criticised opportunism of authorities. Meanwhile Muhammad was led in his actions not but a determined and steady moral code, but acted as a political leader, aiming at holding and expansing his power. His morality was depending on temporary political interest.
 Krzysztof Kościelniak, Dżihad. Święta wojna w islamie, Kraków 2002, s. 24.
 Ibidem, s. 25.
 Ibidem, s. 29.
 Ibidem, s. 28.
The original title: Jihad i Koran
Koran translations from The Noble Qur’an