Here's a stab at beginning to answer this notion, spotted frequently on some of the pro-war blogs I read, that the religion of Islam is inherently and irredeemably toxic. I've been putting this off for a while because for one thing I have limited confidence in my own bloviating on this subject (the sudden discovery of previously unsuspected false assumptions continuing to be a regular and frequent consequence of more reading, with no signs of tapering off), and for another I don't really know where to start.
At the beginning, I guess. Muhammad was a member of the Quraysh tribe residing in Mecca, a small urban community that thrived as a stop along a trade route and as something of a pilgrimage site because a polytheistic temple (the altar of which survives as the Kaaba) was located in the town. He was hired as the agent of a wealthy widow and tradeswoman (Khadija), and would have encountered Jewish and Christian communities while traveling north on her business. Khadija married Muhammad, and became the first convert to Islam when Muhammad told her of his visions of the angel Gabriel. A small number of Meccans converted to Islam (Abu Bakr being the first or one of the first among them, which will become important later), but on the whole monotheism received a cold reception in Mecca, not least because the gods populating the local temple were an important source of commerce from pilgrims. When Muhammad found himself being denounced and derided by members of his own tribe, he and his community of believers accepted an invitation from the Jewish and Christian communities (collectively referred to in the Koran as the Ansar, or "helpers") of Medina to shelter there. This remove is known as the Hejira, and the Muslim calendar dates from the year of this event.
At this point in time, only a small portion of the population of the Arabian peninsula was urbanized. Most Arabs were still organized into Bedouin tribes, and relations between tribes were mostly defined by warfare. Each tribe had its own god, and would routinely raid other tribes for treasure and slaves. The god of the loser would be smashed and repudiated by his or her previous adherents who had escaped the raid intact, and who would then sometimes adopt the god of the victors as evidently the stronger deity.
Muhammad sought to convert the Arabs to Islam by warfare in a similar fashion. For one thing, victory in warfare was the major sign of the efficacy of any god in the minds of the Arabs; for another, monotheism offered the promise, ultimately, of peace. Muhammad's innovation was to offer prisoners of war the option of conversion to Islam and membership in the Muslim community rather than execution or enslavement; his theory was that once all the Arabs were united under the god of Abraham, war itself would cease. In this theory and in this context, warfare for the sake of Islam was understood to be basically defensive, it being only a matter of time before any prosperous community, including any community of Muslims if it gained any traction or success, would be attacked and raided by another under a different banner. (The notion of preemptive "defensive" warfare, with the additional. purpose of creating the conditions for a more permanent peace, will perhaps be familiar to those following current events). In essence, the goal was to replace warring tribal affiliations with shared Muslim confessional identity as the basis of community.
Muhammad launched his military campaign from Medina in the period following the Hejira, and about half the verses of the Koran record the revelations of the Prophet from this period. Most of the Koranic sura announcing murderous intentions towards unbelievers and particularly polytheists date from this period; so does the Dhimmi contractual relationship between Muslims and non-Muslim "peoples of the Book," Jews and Christians. The notion at the time was total warfare against polytheists and death to those who would not convert, but tolerance of Jews and Christians within conquered communities, in recognition partly of their shared confessional relationship to the god of Abraham, and partly of the assistance of the Ansar of Medina. The Dhimmi authorizes a diminished role and certain limitations on the rights of Jews and Christians under Muslim rule; where Jews and Christians resisted Muslim conquest, they were fought and sometimes slaughtered as well. Sura from this period also both authorize the making and honoring of peace contracts with unbelievers, and breaking them when necessary for some strategic purpose or other.
Various Koranic sura relating to the initial Muslim conquest are frequently cited as evidence that Muslims believe they are enjoined by God to be in a state of permanent warfare with non-Muslims until conversion is universal. The notion of jihad, which signifies the faithful struggle towards any goal of the faith, including purely spiritual and ethical ones, is objectified as a central tenet of Islam, and defined primarily as "holy war." Both of these propositions are basically Islamist propaganda; commentators who urge us to "take what our enemies say seriously" err in assuming that these interpretations describe Islam itself rather than Islamism. In fact the word jihad is used in many contexts in the Koran, and the history of Islamic civilization is clearly not one of endless proselytizing warfare.
The Islamist interpretation of the Koran and Hadith represents a deep rupture with traditional Islam, which has been modified and qualified over time within specific political realities, most importantly the gulf that quickly emerged between Muhammad's ideal community of believers and the type of political organization subsequent generations were able to achieve. Muhammad instituted no church and chose no successors; the community of believers would eventually divide permanently over questions of succession and political legitimacy, and ultimately the story of assassinations and civil war surrounding these events would become, in Muslim consciousness, a story about why the Muslim community had a Caliph rather than an Imam at its head.
Following the death of Muhammad, the Companions of the Prophet decided to select Abu Bakr as successor to Muhammad's political and spiritual headship of the Muslim community. Abu Bakr was both an early convert to Islam, and the father of Aisha, one of Muhammad's wives (who had collectively been given the title Mothers of the Believers by Muhammad during his lifetime). Some members of the community felt that Ali ibn Abi Talib, both a cousin of Muhammad's and the husband of his daughter Fatima (the only child of Muhammad to both survive to adulthood and produce male progeny, Hasan and Husayn), and an early convert, should have succeeded, but he was passed over two more times, following the natural death of Abu Bakr a year later. Umar, another father-in-law of Muhammad's and an early Qurayshi convert, followed; his rule was ended with his death by private vengeance. Uthmann, another Qurayshi early Companion related to Muhammad by marriage was next. He was assassinated for political reasons; supporters of Ali were suspected. When Ali was finally chosen as successor, Aisha led the opposition to him in the Battle of the Camel, the first Muslim civil war. Aisha's faction was crushed, but Mu'awiya ibn Abi Sufyan, a close kinsman of Uthmann's (and a somewhat distant one of Muhammad's), challenged Ali's rule. After the two parties fought to a draw, they entered a period of negotiation during which Ali was assassinated, whereupon Mu'awiya assumed the Caliphate. Succession was basically hereditary from this point forward, passing from the Umayyad to the Abbasid branch of the Quraysh about a hundred years later.
Abu Bakr, Umar, Uthmann, and Ali are regarded as the Four Rightly-Guided Caliphs of Islam, or el-Rashidun, by Sunni Muslims; Shia, or "partisans of Ali," regard the first three as usurpers, and Ali and his descendants as the rightful heirs to Muhammad's leadership of the community of Muslims (or Ummah). Both groups regard the Umayyads and the Caliphs who succeeded them as usurpers, but made their peace with this political reality in different ways.
Sunni Muslims base their belief in the legitimacy of the first four on their status as those selected by the consensus of the community arising from mutual consultation and deliberation (shura), and to a wealth of Hadith literature indicating Muhammad's preference for Abu Bakr during his lifetime, which Shia Muslims reject. The ascension of the Umayyads and the hereditary caliphate robbed the ulema (originally Companions of the Prophet and later the religious scholars who succeeded in their capacity as spiritual leaders of the Ummah) of their role in selecting their own political leader. However, the ulema elected to accept Mu'awiya's rule rather than engage in further warfare. This decision was based on numerous warnings against fitna, or rebellion, found in the Koran, and on a Koranic sura enjoining Muslims to obey "those who rule over you." From the ascension of Mu'awiya forward, Sunni Muslims have not regarded the Caliph as the spiritual leader or Imam of the Ummah in the way that Muhammad and the Rashidun were. Instead, the Caliph was required only to be a Muslim and to act as a sort of custodian of Islam, instituting the Shari'a through his courts and providing a social order within which Islam could flourish. The ulema would act as intermediaries between the people and their ruler, and would in some cases act as government officials, for example as judges in Shari'a courts, but would never again have a direct role in governing. In fact entire areas of administrative, commercial and civil law were instituted that had no relationship to Shari'a, the Koran being silent on many matters that concern an empire. (The Sunni attitude towards the caliphate somewhat resembled the European notion of the divine right of kings, though the ulema never had even a ceremonial role in legitimizing each new ruler).
Shia Muslims, in contrast, have never been so accepting of the authority of the Caliph, but can trace the bloodline of Ali only to his 12th descendant, Muhammad al-Muntazar, who disappeared in 874. There are many different Shia sects, but the largest one believes that this hidden or occulted Imam will someday reappear as the Mahdi, to provide legitimate and true guidance to the Ummah once again. The nature of this expectation is somewhat similar to that of Christians for the Second Coming; not even Ayatollah Khomeini dared to claim the title (though some of the more sycophantic mullahs would give it to him from time to time). The notion of the occulted Imam permits Shia Muslims to tolerate imperfect and Islamically illegitimate rulers while they wait; their traditional political stance has been quietism coupled with a culture of vigorous Islamic interpretation and debate to supply the missing guidance of the Mahdi.
Some aspects of the two foregoing paragraphs, it strikes me, might be revisionist history. There is some evidence that the Umayyads at least regarded themselves as rightful successors to Muhammad, and the mainstream of Islamic scholarship did not begin calling itself Sunni ("of the tradition") and the partisans of Ali Shia until the 4th century of Islamic scholarship. Previously, Shiism had merely been a stubborn and growing strain of criticism of the Muslim status quo. Sunni representation of the immediate period following the death of the Prophet may well be an attempt to legitimate the actual political development of this status quo long after the fact, in a way that accommodated the most stinging of Shia criticism while holding onto the legitimacy of the Rashidun by treating the ascension of the Umayyads rather than that of Abu Bakr as the critical change-point in Islamic leadership. Certainly representation of pivotal figures in the crisis of succession such as Aisha underwent substantial revision in medieval Muslim scholarship in a similar attempt to incorporate Shia criticism while maintaining the authority of Abu Bakr and Aisha and all the Hadith attributed to their authority. But for our purposes the point is how this way of understanding the Muslim past legitimated the disconnect between religious and political authority in the entire ensuing history of Islamic civilization, until the 20th Century.
That history is difficult to summarize. Following the Abbasid dynasty, the Caliphate breaks up a bit--in his industrious youth Mr. Bell Jar made a chart of all the dynasties that ruled all the various lands of Islamic civilization throughout its history, and between the monochrome Abbasids and Ottomans is a riot of color--but in general, Muhammad had united the Arabian peninsula during his lifetime, and subsequent rulers continued the expansion, though the lands of Islam were not always united under one Caliph. The name of jihad was given to many of these wars of conquest, but in most instances they were undertaken for the same reason any empire expands: acquisition of wealth and territory, strategic protection of existing possessions, etc. The notion of jihad in this history reflects imperial confidence in the superiority of its own rule over that existing in the lands it is conquering rather than a fanatical religious motivation for warfare. The idea of the Caliph as an Imam with a revolutionary and universalizing religious/political agenda was buried on the other side of the death of Ali, or so successors to the Caliphate must have hoped.
And so it stood for about 1400 years, more or less. (To be continued later, maybe ...)