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The second fitnah lasted from 680-692 CE and is usually agreed to have begun with the failed attempt at revolution by Husayn. Husayn was the grandson of the prophet through his only daughter, Fatimah, the wife of 'Ali. He was invited to the town of Kufah in 680 CE to begin a revolt, but the Syrian governor of the town was able to scare the people of Kufah out of supporting him by the time he arrived in town. Without the support of the townspeople of Kufah, Husayn's miniscule personal forces, which refused to submit to the rule of the caliph, were easily wiped from the face of the earth in the desert outside Karbala by the forces of the Syrian caliph, Mu'awiyah's son Yazid, against whom the hypothetical rebellion would have been waged. Husayn was seen as a holy personage, though, especially by the Shi'is, who viewed Muhammad's line as being especially close to God. With this regrettable occurence, the second major round of civil wars in the Islamic world began.

Possibly spurred on by Husayn's example (my sources are ambiguous on this; /msg me if your information is more conclusive), 'Abd-Allah Ibn al-Zubayr raised a revolt in 681 in the heart of the Islamic world, Mecca and Medina. The caliph Yazid waged war against his forces until 683, when they took Medina at the Battle of the Harrah and laid siege to Mecca. Victory looked to be close at hand for the caliph, but then he died in 683. His only son, Mu'awiyah II, died shortly thereafter. The Dar al-Islam was left without a leader, so they turned to the next best candidate, Ibn al-Zubayr. He was generally recognized as caliph, despite his former status as a rebel.

Unfortunately, rivalries between groups, especially the Qays and Kalb tribal factions, conspired to ensure that the peace would be short-lived. The Kalb, a tribal bloc that had supported Mu'awiyah strongly, came to violence with the Qays, a group that supported Ibn al-Zubayr. At Marj Rahit the Kalb overcame the Qays in 684 to establish Marwan, chief advisor to 'Uthman as well as a cousin of Mu'awiyah's, as counter-caliph in much of Syria, from which he then expanded into Egypt.

The Syrians were not the only group opposed to the rule of Ibn al-Zubayr, though. Also in 684, the Kharijis, a few of whom had supported Ibn al-Zubayr for a time, raised two separate rebellions in Iran and Arabia. Those in Iran, known as Azraqi Kharijis, believed that all who did not adhere to their beliefs should die. They were the strongest of a number of contending forces in the area for quite some time. Those in Arabia actually took control of much of the Eastern coast, setting up a tax structure and generally laying down the framework for a Khariji state. At the same time, the Kufan Shi'is set out to attack the Syrians in revenge for Husayn's death and set up one of 'Ali's other sons, Ibn-al-Hanafiyyah as ruler from Kufah in 685. This rebellion was put down in the name of Ibn al-Zubayr in 687 by his brother Mus'ab, who took effective rulership of the area as governor.

In Syria, the counter-caliph Marwan died, leaving his son 'Abd al-Malik the counter-caliphate. Drawing on their old loyalties as well as their superior authoritarian organization, the forces of 'Abd al-Malik managed to reconquer the rest of the Dar al-Islam. From their starting point in Syria, the armies first took Kufah back by force from Mus'ab in 691. They then swept into the Arabian peninsula itself, ejecting the Kharijis from power before finally removing Ibn al-Zubayr from power. In the battle, which was waged by al-Hajjaj at Mecca in 692, the Ka'bah, the most holy structure in all of Islam, was destroyed along with Ibn al-Zubayr. The Ka'bah was rebuilt, while Ibn al-Zubayr was not so fortunate.

The Syrians managed to reestablish their former power structure reasonably quickly after 'Abd al-Malik took power, although the Iranian Kharijis were not finally defeated until 699, when the governor of the Iraq destroyed them utterly. The main historical result of all of this conflict was the establishment of a long-term Syrian power base on which the Marwani caliphs were able to draw for decades thereafter, although the animosities that surfaced during this time between the many groups involved formed something of a legacy as well, forming new conflicts between Qays and Kalb, Shi'is and Sunnis (whose respective identities had been established during the first fitnah but not crystallized until the second), and the Kharijis and everyone else for years to come.

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