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If we’re going to talk about the end of the Assassin order, we should probably talk about who they were first. You may already know something about them—of all the topics one can cover in Islamic history, they're one of the most provocative and interesting to Western audiences. There's even a whole video game series about the Assassins, or about very fictionalized version of them, anyway. The truth is a little drier than some of the stories you may have heard, but isn't that always the way?
The Assassin order's origins go back to the Fatimid Caliphate that ruled Egypt and Syria from the early 10th century through the late 12th century. The Fatimids were Shiʿa, of the Ismaʿili branch, which formed in the schism that followed imam Jafar al-Sadiq's death in 765. It was another schism that led to the formation of the Assassin order, this time following the death of Fatimid Caliph al-Mustansir Billah in 1094. Mustansir was initially succeeded by his elder son, Nizar (d. 1097), but the powerful Fatimid vizier al-Afdal (d. 1121) decided that he would prefer to have Mustansir’s younger and more pliable son, al-Mustaʿli (d. 1101), on the throne. By this point, the Fatimids’ viziers were more powerful than the Fatimids caliphs were, so al-Afdal’s will was done.
Nizar had his supporters though. One, an especially zealous Ismaʿili convert named Hasan-i Sabah (d. 1124), headed to Iran, where there were small Ismaʿili communities all over the place (the Ismaʿilis were fantastic missionaries), especially in the east and around the southern coast of the Caspian Sea. Disconnected as these communities were from the day-to-day happenings at the Fatimid court, they made a pretty fertile ground from which Hasan could recruit followers. But they needed a base of operations. Hasan was operating in Seljuk territory and was apparently known to Seljuk authorities, who wanted to arrest him and, probably, execute him. So he needed a very defensible and hopefully fairly remote place to call home, and he set his sights on assuming ownership of the castle at Alamut, just north of the city of Qazvin near the Caspian, as you can see on the map:
Hasan took his time, sending followers to infiltrate the village below the fortress and eventually to gain work inside the fortress itself. By the summer of 1090, when Hasan himself entered the castle, so many of the castle’s garrison and staff were his people that he was able to take it from its lord without a fight.
The Nizaris went on to capture a number of other castles in much the same way, such that they can be thought of as a state within a state—within two states, actually, since they had fortresses inside both the Seljuk empire and the Fatimid Caliphate (later the Ayyubid sultanate)—operating in shadow with the authorities alternately hunting them and hiring them. The castles were chosen for their defensibility in a siege, but the Assassins preferred not to engage in pitched battle. Their specialty was—wait for it—assassination. Hasan’s soldiers (the lowest level of Nizari adherents) were called fidaʾiyin (“fedayeen” in the more modern rendition), which means “people willing to sacrifice themselves.” They were singularly devoted to the cause for reasons we don't entirely understand. Marco Polo claimed that they were drugged with hash and convinced they’d been given a glimpse of paradise and could only return if they carried out their orders, but it’s unlikely Marco Polo actually had any idea what he was talking about so this claim is generally disregarded. But they were very literally prepared to die in the course of their assassination missions, and that combined with their training made them quite formidable.
They were so formidable, in fact, that they were able to kill the powerful Seljuk vizier, Nizam al-Mulk, in October 1092, and his boss, Sultan Malik Shah I, in November 1092. Those two murders established the order’s reputation and were the reason why the Assassins survived for another 160-plus years and weren’t squashed in their early days by the Seljuk authorities. Their reputation grew along with each of their murders, to the point where a) the Seljuks stopped hunting them because sultans began to fear becoming their next target, and b) virtually any political murder in the Middle East was invariably attributed to the Assassins. When the Crusaders arrived in the region just a couple of years later, as you can imagine there were a lot of politically-related murders that started taking place for which the Assassins got credit even though they may not actually have been responsible. It was through the reporting of the Crusaders that the Assassins’ reputation for fanaticism and self-sacrifice was solidified—and almost certainly embellished a fair bit.
Such was the Assassins’ reputation by the middle of the 13th century that when Genghis Khan’s grandson, Möngke (d. 1259), became Great Khan of the Mongolian Empire in 1251 and later sent his brother, Hulagu (d. 1265), west to invade the Middle East, it was with two orders: meet with the Abbasid caliph in Baghdad and destroy the Assassins. Well, OK, it was their reputation that prompted this order combined with the fact that they’d apparently made one or possibly several attempts on Möngke’s life (sources diverge on this point). Hulagu eventually destroyed Baghdad because the caliph refused to meet with him and pay homage, but that was in 1258, two years after he’d already wiped out the Assassins.
The end came pretty suddenly. As I said above, the Assassins’ fortresses were selected and designed to be defensible against the Seljuks, but they simply weren't defensible against a large Mongolian army with advanced Chinese siege gear and enough soldiers to starve their garrisons out if push came to shove. The Mongols dispatched an army west under one of their senior generals, Kitbuqa, in 1253, and he captured several Assassin fortresses (though one, Girdkuh, actually held out until 1270) before being joined by a larger force, under Hulagu's direct command, in 1256.
The combined army marched on the remaining Assassin castles in Iran, and in response the brand new Nizari imam, Rukn al-Din Khurshah (d. 1256, and no that’s not a coincidence), started dismantling the defenses at Alamut and at the nearby fortress of Maymundiz (where he was located) and Lamassar, in a show of submission to the Mongol invaders. Hulagu besieged Maymundiz anyway, on November 8, and on November 19 Rukn al-Din left the castle to surrender to the Mongols. The Assassin order was finished, at least in Mongolian territory. Rukn al-Din sent word to the other two castles to surrender, and on December 15 the Mongols entered Alamut, where the Assassin order had begun, and destroyed it. Rukn al-Din was put to death for his trouble, perhaps on the advice of some of the Mongols’ own Muslim advisors who believed the Nizaris to be particularly contemptible heretics.
A branch of the Assassin order did survive in Syria, outside of Mongolian control, but it was basically deputized by the Mamluk Sultan Baybars in the 1270s and thereafter its fighters did the Mamluks’ bidding in return for being allowed to, well, stay alive. Some scholars of Sufism in the late medieval period believe that you can trace the subsequent rise of organized Sufi schools, several of which eventually became militant, to the dissemination of some of the Assassins’ tenets or at least their organizational ideas throughout the Sufi community following their defeat, but as far as I know historians are far from a consensus on that point. The modern Nizari community doesn't dabble in assassination anymore, but it is the largest Ismaʿili branch in the world under its leader, known as the Aga Khan.