One of the most striking passages in the Qur’an is 2:106, which provides the basis for the doctrine of abrogation:
“We do not abrogate a verse or cause it to be forgotten except when We bring forth one better than it or similar to it. Do you not know that Allah is over all things competent?”
Allah, in other words, changes revelations as he goes along, and the later revelations supersede the earlier ones. There is disagreement among Muslim theologians as to exactly which verses have been abrogated and replaced, but the general idea has been clear. When Muslims are weak and in a minority position, they should behave peacefully according to the Meccan passages (which reflect the early time when Muhammad was vulnerable and building his power base), and when strong, they are obligated to wage war according to the later Medinan passages (written when Muhammad was in power).
The suras of the Qur’an obviously aren’t in chronological order (for a reconstruction see here). The ninth sura, known as the Ultimatum, is the latest revelation and takes precedence over all. Muhammad received it the year before his death (631 AD), when he was at his strongest, and it’s here that we get the famous verse of the sword, which commands Muslims to kill pagans unless they convert to Islam (Qur’an 9:5). Jews and Christians must also convert or die, though they are allowed a third option, to become subjugated “with willing submission” by paying the jizya (a head tax) as second-class citizens (Qur’an 9:29). Wayward Muslims — hypocrites, liberals and heretics of different sects — are also to be killed (Qur’an 9:73). True Muslims enforce all of this. They are to kill infidels and heretics until they die in martyrdom (Qur’an 9:111).
Groups like ISIS take direct inspiration from these and other late suras, such as the fifth: “The punishment for those who wage war against Allah and His Messenger and strive to make mischief in the land is none but that they be killed or crucified or that their hands and feet be cut off from opposite sides or that they be imprisoned. That is for them a disgrace in this world; and for them in the Hereafter will be a grievous punishment.” (Qur’an 5:33) “Making mischief” is something that can mean almost anything to justify said killing, crucifying, etc. Mere unbelief can be construed as mischief and has been.
Another late revelation is the forty-seventh, which explicitly forbids Muslims to seek peace when they have the wherewithal to wage war. “Do not weaken and call for peace when you should be uppermost” (Qur’an 47:35). Muslims who live in western nations are exempt from this command, because they are not in a superior (uppermost) position, but those, say, in Iraq or Syria, are obligated to not seek peace; they must wage war. Likewise, Muslims living in secular Islamic states (i.e. under the Shah in pre-1979 Iran) are exempt from the command, but once fundamentalist figures (like the Ayatollah) gain power, they must wage war.
When modern liberal Muslims cite “there is no compulsion in religion” (Qur’an 2:256) and that if you disagree with someone, “to you be your religion and to me be mine” (Qur’an 109:6), we should of course applaud them. But theirs is an uphill battle, because the doctrine of abrogation refutes their citations in advance. To my knowledge, there is nothing comparable to this phenomenon in the scriptures of other religions. When rabbis debated whether or not children suffer punishment for the sins of their parents, there is no controlling text within the Jewish scriptures that would lead one to favor Exodus 20:5 (“yes”) over Ezekiel 18:20 (“no”), or vice-versa. That’s what makes most scriptures conveniently malleable.
Islam provides little enough ammunition to counter its unpleasant elements as it is. So it’s all the more troubling that what little it does provide has been rendered obsolete by that very tradition. The Islamic reformer Mahmoud Muhammad Taha was killed for essentially trying to reverse the doctrine of abrogation, and make the Qur’an’s early revelations supersede the later ones. This all adds up to a significant difference between the scriptures of Islam and those of other religions.