Sieges of Bukhara, Samarkand, and Urgench
Genghis placed his general Jebe at the head of a small army sent to the south, intending to cut off any retreat by the Shah to that half of his kingdom. Further, Genghis and Tolui, at the head of an army of roughly 50,000 men, skirted Samarkand and went westwards to lay siege to the city of Bukhara first. To do this, they traversed the seemingly impassable Kyzyl Kum desert by hopping through the various oases, guided most of the way by captured nomads. The Mongols arrived at the gates of Bukhara virtually unnoticed. Many military tacticians regard this surprise entrance to Bukhara one of the most successful surprise attacks in warfare.
Bukhara was not heavily fortified, with a moat and a single wall, and the citadel typical of Khwarezmi cities. The Bukharan garrison was made up of Turkish soldiers and led by Turkish generals, who attempted to break out on the third day of the siege. The break-out force, of perhaps 20,000 men, was annihilated in open battle. The city leaders opened the gates to the Mongols, though a unit of Turkish defenders held the city's citadel for another twelve days. Survivors from the citadel were executed, artisans and craftsmen were sent back to Mongolia, young men who had not fought were drafted into the Mongolian army and the rest of the population was sent into slavery. As the Mongol soldiers looted the city, a fire broke out, razing most of the city to the ground. Genghis Khan had the people assemble in the main mosque of the town, where he declared that he was the flail of God, sent to punish them for their sins before ordering their execution.
After the fall of Bukhara, Genghis headed to the Khwarezmi capital of Samarkand and arrived in March 1220. Samarkand possessed significantly better fortifications and as many as 100,000 men defending. As Genghis began his siege, his sons Chaghatai and Ögedei joined him after finishing the reduction of Otrar, and the joint Mongol forces launched an assault on the city. The Mongols attacked using prisoners as body shields. On the third day of fighting, the Samarkand garrison launched a counterattack. Feigning retreat, Genghis drew a garrison force of 50,000 outside the fortifications of Samarkand and slaughtered them in open combat. Shah Muhammad attempted to relieve the city twice, but was driven back. On the fifth day, all but an approximate 2,000 soldiers surrendered. The remaining soldiers, die-hard supporters of the Shah, held out in the citadel. After the fortress fell, Genghis reneged on his surrender terms and executed every soldier that had taken arms against him at Samarkand. The people of Samarkand were ordered to evacuate and assemble in a plain outside the city, where they were killed and pyramids of severed heads raised as the symbol of Mongol victory.
About the time of the fall of Samarkand, Genghis Khan charged Subutai and Jebe, two of the Khan's top generals, with hunting down the Shah. The Shah had fled west with some of his most loyal soldiers and his son, Jalal al-Din, to a small island in the Caspian Sea. It was there, in December of 1220, that the Shah died. Most scholars attribute his death to pneumonia, but others cite the sudden shock of the loss of his empire.
Meanwhile, the wealthy trading city of Urgench was still in the hands of Khwarezmian forces. Previously, the Shah's mother had ruled Urgench, but she fled when she learned her son had absconded to the Caspian Sea. She was captured and sent to Mongolia. Khumar Tegin, one of Muhammad's generals, declared himself Sultan of Urgench. Jochi, who had been on campaign in the north since the invasion, approached the city from that direction, while Genghis, Ögedei, and Chaghatai attacked from the south.
The assault on Urgench proved to be the most difficult battle of the Mongol invasion. The city was built along the river Amu Darya in a marshy delta area. The soft ground did not lend itself to siege warfare, and there was a lack of large stones for the catapults. The Mongols attacked regardless, and the city fell only after the defenders put up a stout defense, fighting block for block. Mongolian casualties were higher than normal, due to the unaccustomed difficulty of adapting Mongolian tactics to city fighting.
The taking of Urgench was further complicated by continuing tensions between the Khan and his eldest son, Jochi, who had been promised the city as his prize. Jochi's mother was the same as his three brothers': Genghis Khan's teen bride, and apparent lifelong love, Borte. Only her sons were counted as Genghis's "official" sons and successors, rather than those conceived by the Khan's 500 or so other "wives and consorts." But Jochi had been conceived in controversy; in the early days of the Khan's rise to power, Borte was captured and raped while she was held prisoner. Jochi was born nine months later. While Genghis Khan chose to acknowledge him as his oldest son (primarily due to his love for Borte, whom he would have had to reject had he rejected her child), questions had always existed over Jochi's true parentage.
Such tensions were present as Jochi engaged in negotiations with the defenders, trying to get them to surrender so that as much of the city as possible was undamaged. This angered Chaghatai, and Genghis headed off this sibling fight by appointing Ögedei the commander of the besieging forces as Urgench fell. But the removal of Jochi from command, and the sack of a city he considered promised to him, enraged him and estranged him from his father and brothers, and is credited with being a decisive impetus for the later actions of a man who saw his younger brothers promoted over him, despite his own considerable military skills.
As usual, the artisans were sent back to Mongolia, young women and children were given to the Mongol soldiers as slaves, and the rest of the population was massacred. The Persian scholar Juvayni states that 50,000 Mongol soldiers were given the task of executing twenty-four Urgench citizens each, which would mean that 1.2 million people were killed. While this is almost certainly an exaggeration, the sacking of Urgench is considered one of the bloodiest massacres in human history.
Then came the complete destruction of the city of Gurjang, south of the Aral Sea. Upon its surrender the Mongols broke the dams and flooded the city, then proceeded to execute the survivors.
Read more about this topic: Mongol Invasion Of Khwarezmia