While other scriptures contain contradictions, the Koran is the only holy book whose commentators have evolved a doctrine to account for the very visible shifts which occur from one injunction to another. No careful reader will remain unaware of the many contradictory verses in the Koran, most specifically the way in which peaceful and tolerant verses lie almost side by side with violent and intolerant ones. The ulema were initially baffled as to which verses to codify into the Shari’a worldview—the one that states there is no coercion in religion (2:256), or the ones that command believers to fight all non-Muslims till they either convert, or at least submit, to Islam (8:39, 9:5, 9:29). To get out of this quandary, the commentators developed the doctrine of abrogation, which essentially maintains that verses revealed later in Muhammad’s career take precedence over earlier ones whenever there is a discrepancy. In order to document which verses abrogated which, a religious science devoted to the chronology of the Koran’s verses evolved (known as an-Nasikh wa’l Mansukh, the abrogater and the abrogated).
But why the contradiction in the first place? The standard view is that in the early years of Islam, since Muhammad and his community were far outnumbered by their infidel competitors while living next to them in Mecca, a message of peace and coexistence was in order. However, after the Muslims migrated to Medina in 622 and grew in military strength, verses inciting them to go on the offensive were slowly “revealed”—in principle, sent down from Allah—always commensurate with Islam’s growing capabilities. In juridical texts, these are categorized in stages: passivity vis-á-vis aggression; permission to fight back against aggressors; commands to fight aggressors; commands to fight all non-Muslims, whether the latter begin aggressions or not.  Growing Muslim might is the only variable that explains this progressive change in policy.
Other scholars put a gloss on this by arguing that over a twenty-two year period, the Koran was revealed piecemeal, from passive and spiritual verses to legal prescriptions and injunctions to spread the faith through jihad and conquest, simply to acclimate early Muslim converts to the duties of Islam, lest they be discouraged at the outset by the dramatic obligations that would appear in later verses. Verses revealed towards the end of Muhammad’s career—such as, “Warfare is prescribed for you though you hate it”—would have been out of place when warfare was actually out of the question.
Allah himself speaking through the Koran justifies abrogation: “Whenever We abrogate a verse or cause it to be forgotten, we replace it by a better or similar one. Know you not that Allah has power over all things?” (Koran 2: 106; see also 16:101, 13:39, and 17:86).
However interpreted, the standard view on Koranic abrogation concerning war and peace verses is that when Muslims are weak and in a minority position, they should preach and behave according to the ethos of the Meccan verses (peace and tolerance); when strong, however, they should go on the offensive on the basis of what is commanded in the Medinan verses (war and conquest). The vicissitudes of Islamic history are a testimony to this dichotomy, best captured by the popular Muslim notion, based on a hadith, that, if possible, jihad should be performed by the hand (force), if not, then by the tongue (through preaching); and, if that is not possible, then with the heart or one’s intentions.
Consider the role of deceit or taqiyya in Islam in the context of jihad and abrogation. That Islam legitimizes deceit during war is, of course, not all that astonishing; after all, as the Elizabethan writer John Lyly put it, “All’s fair in love and war.” Other non-Muslim philosophers and strategists—such as Sun Tzu, Machiavelli, and Thomas Hobbes—justified deceit in warfare. Deception of the enemy during war is only common sense. The crucial difference in Islam, however, is that war against the infidel is a perpetual affair—until, in the words of the Koran, “all chaos ceases, and all religion belongs to Allah.” In his entry on jihad from the Encyclopaedia of Islam, Emile Tyan states: “The duty of the jihad exists as long as the universal domination of Islam has not been attained. Peace with non-Muslim nations is, therefore, a provisional state of affairs only; the chance of circumstances alone can justify it temporarily.”
Moreover, going back to the doctrine of abrogation, Muslim scholars such as Ibn Salama (d. 1020) agree that Koran 9:5, known as ayat as-sayf or the sword verse, has abrogated some 124 of the more peaceful Meccan verses, including “every other verse in the Koran, which commands or implies anything less than a total offensive against the nonbelievers.” In fact, all four schools of Sunni jurisprudence agree that “jihad is when Muslims wage war on infidels, after having called on them to embrace Islam or at least pay tribute [jizya] and live in submission, and the infidels refuse.”
It is the same with Koran 9:29—the final word on the fate of Christians and Jews, and the divine source behind the idea that they must always live in subjugation to Muslims: Allah commands believers to “Fight those among the People of the Book who do not believe in Allah nor the Last Day, nor forbid what Allah and His Messenger have forbidden, nor embrace the religion of truth [i.e., Islam], until they pay the jizya [tribute] with willing submission and feel themselves subdued.”
In Islamic parlance, “People of the Book” is a reference to those pre-Islamic peoples who had their own scriptures—chief among them, Christians and Jews. Koran 9:29, and its equally bellicose counterpart, Koran 9:5, appeared as Muhammad’s armies were preparing to invade the Christian territories of the Byzantine empire.
A year after proclaiming these anti-Christian verses, Muhammad was dead, revelations ceased, and the Islamic jihad against the surrounding infidels, most of whom were Christians, erupted from Arabia, in the first phase of what are commonly known as the Muslim conquests of history. Till this day, mainstream Islamic jurisprudence holds that the Sword Verses (specifically 9:5 and 9:29) have “abrogated, canceled, and replaced 124 verses that called for tolerance, compassion, and peace.
The obligatory jihad is best expressed by Islam’s dichotomized worldview that pits the realm of Islam against the realm of war. The first, dar al-Islam, is the “realm of submission,” the world where Shari’a governs; the second, dar al-Harb (the realm of war), is the non-Islamic world. A struggle continues until the realm of Islam subsumes the non-Islamic world—a perpetual affair that continues to the present day. The renowned Muslim historian and philosopher Ibn Khaldun (d. 1406) clearly articulates this division:
In the Muslim community, jihad is a religious duty because of the universalism of the Muslim mission and the obligation to convert everybody to Islam either by persuasion or by force. The other religious groups did not have a universal mission, and the jihad was not a religious duty for them, save only for purposes of defense. But Islam is under obligation to gain power over other nations.
 Ibn Qayyim, Tafsir, in Abd al-’Aziz bin Nasir al-Jalil, At-Tarbiya al-Jihadiya fi Daw’ al-Kitab wa ‘s-Sunna (Riyahd: n.p., 2003), pp. 36-43.
 Mukaram, At-Taqiyya fi ’l-Islam, p. 20.
 Koran 2: 216.
 Yahya bin Sharaf ad-Din an-Nawawi, An-Nawawi’s Forty Hadiths, p. 16, accessed Aug. 1, 2009.
 John Lyly, Euphues: The Anatomy of Wit (London, 1578), p. 236.
 Koran 8:39.
 Emile Tyan, The Encyclopedia of Islam (Leiden: Brill, 1960), vol. 2, s.v. “Djihad,” pp. 538-40.
 David Bukay, “Peace or Jihad? Abrogation in Islam,” Middle East Quarterly, Fall 2007, pp. 3-11, f.n. 58; David S. Powers, “The Exegetical Genre nasikh al-Qur’an wa-mansukhuhu,” in Approaches to the History of the Interpretation of the Qur’an, Andrew Rippin, ed. (Oxford: Clarendon Press, 1988), pp. 130-1.
 Jalil, At-Tarbiya al-Jihadiya fi Daw’ al-Kitab wa ‘ s-Sunna, p. 7.
 David Bukay, “Peace or Jihad? Abrogation in Islam,” Middle East Quarterly, Fall 2007, pp. 3-11.
 Ibn Khaldun, The Muqadimmah. An Introduction to History, Franz Rosenthal, trans. (New York: Pantheon, 1958), vol. 1, p. 473.