The Second Fitna had been tearing the caliphate apart since 680. When the Umayyad caliph Yazid I died in late 683, the empire cracked in half. Most provinces recognized Abd Allah ibn al-Zubayr, an early companion's son, who ruled from Mecca's sanctuary. Syria's pro-Umayyad tribes rallied around Marwan ibn al-Hakam, and after Marwan's death in 685 his son Abd al-Malik inherited the task of reconquering an empire that had slipped out of the family's hands. By 691, after defeating Ibn al-Zubayr's brother Mus'ab at the Battle of Maskin, Abd al-Malik had crushed every rival except one. The old man in Mecca still refused to bow.

Hajjaj ibn Yusuf arrived at Mecca on 25 March 692 with two thousand Syrian troops, reinforced a month later by Tariq ibn Amr's men from Medina. The orders from Damascus were careful: besiege, starve, avoid bloodshed in the sanctuary. Hajjaj positioned his catapults on Abu Qubays, the mountain overlooking the city, and began a bombardment that would last six or seven months. Supplies were cut. Hunger spread through the defenders. According to the ninth-century historian Baladhuri, when Hajjaj's troops aimed at the Ka'ba itself and a sudden thunderstorm rolled over the mountain, the soldiers panicked at what they took for divine wrath. Hajjaj dismissed the storm as a natural phenomenon and, if anything, read it as an omen of victory. The bombardment resumed.

Ten thousand of Ibn al-Zubayr's men eventually surrendered, including two of his own sons, as Hajjaj offered amnesty to anyone who came over. The old caliph was running out of options. He went to his mother, Asma bint Abi Bakr, and asked whether he should submit. The account, preserved in Muslim tradition, has her refusing to let him fold. She reminded him of his age, of the men who had already died for his cause, and told him to fight. He did. On 4 October or 3 November, the dates are reported variously, Ibn al-Zubayr charged out against Hajjaj's army with his youngest son and a handful of followers. He was killed in the fighting. His head went to the caliph. His body was hung from a gibbet in the city he had held for nine years.

The year was called the Year of Unity. The civil war was over. Hajjaj became governor of the Hejaz, Yemen, and central Arabia, and the caliphate was whole again under Abd al-Malik. But the Ka'ba was scarred, walls cracked where catapult stones had struck. Ibn al-Zubayr had earlier rebuilt the shrine after the 683 fire, changing the square plan to a rectangle to include the hatim, adding a second doorway, claiming he was honoring a wish of Muhammad himself. On Abd al-Malik's orders, Hajjaj now demolished that version and rebuilt the Ka'ba to its earlier plan. The shrine that pilgrims circumambulate today traces directly to this reconstruction. Baladhuri records that Abd al-Malik later regretted the order and wished he had left Ibn al-Zubayr's design in place.

The siege of 692 did not end Mecca, or Islam, or the hajj. Within weeks of Ibn al-Zubayr's death, pilgrims were again circling the rebuilt Ka'ba. But the image of an Umayyad general bombarding the sanctuary during the pilgrimage season entered the historical memory and did not leave. Muslim historians writing under the Abbasids, who overthrew the Umayyads in 750, preserved the accounts with particular attention. The damage done to Abd al-Malik's reputation outlasted his political triumph. Hajjaj would go on to become one of the most feared governors in Islamic history, serving the Umayyads for another twenty years. The Ka'ba he rebuilt is the one still at the center of the world's largest annual pilgrimage.