The Mongol Empire’s Chagatai Khanate comprises the lands controlled by Genghis Khan’s second son, the late Chagatai Khan.

Chagatai's ulus, or hereditary territory, consists of the part of the Empire that extends from the Ili River (today in eastern Kazakhstan) and Kashgaria (in the western Tarim Basin) to Transoxiana (modern Uzbekistan and Turkmenistan). (These territories will later become the Turco-Mongol states.

Apart from problems of lineage and inheritance, the Mongol Empire will continue to be endangered by the great cultural and ethnic divide between the Mongols themselves and their mostly Islamic Turkic subjects; the Chagatai Khanate will by 1369 be conquered by Timur, aka Tamerlane, in his attempt to reconstruct the Mongol Empire.)

Chagatai’s grandson Qara Hülëgü, head of the ulus of the Chagatai Khanate, had in 1246 been deposed by the Grand Khan Güyük Khan and replaced with one of Qara Hulagu's uncles, Yesü Möngke.

Qara Hülëgü has gained the Great Khan's favor, however, by supporting him in his purges of the family of the late Ögedei Khan.

Restored in 1252 to his position of Chagatai Khan, Qara Hülëgü dies before returning to his realm and is succeeded by his son Mubarak Shah, with his mother, Orghana Khatun, acting as regent.

Both she and Mubarak Shah rule as Muslims.

The Great Khan claimant Ariq Böke had in 1260 appointed Chagatai Khan's son Alghu, and by the following year Alghu had assumed control over much of the Khanate.

When Alghu revolts against Ariq Böke in 1262, Organa supports him.

In attempting to intervene in the affairs of the White Horde, the Mongol khanate north of the Aral Sea, Ariq Böke evokes a military response from Hulagu, the Il-Khan ruler of Persia.

The Chagatai Khanate had undergone a transformation after the Chagatayid Qazan Khan was killed in 1346.

In the west (Transoxiana), the mostly Turko-Mongol tribes, led by the Qara'unas amirs, have seized control.

In order to maintain a link to the house of Genghis Khan, the amirs have set several of his descendants on the throne, though these khans rule in name only and have no real power.

The eastern part of the khanate, meanwhile, has been largely autonomous for several years as a result of the khans' weakening power.

This eastern portion (most of which is known as "Moghulistan") is, in contrast to Transoxiana, primarily inhabited by Mongols and is largely Buddhist and Shamanist.

The most powerful family in the eastern part of the khanate during this time is a Mongol one, that of the Dughlat amirs.

The Dughlats hold several important towns as vassals to the khans, including Kashgar, Aksu, Yarkand, and Khotan.

The Dughlat amir Bulaji, after seeing the situation in Transoxiana, had decided in around 1347 to raise a khan of his own choosing.

His choice had fallen on Tughlugh Timur, who was at that time little more than an adventurer.

Tughlugh was converted by a Muslim cleric Mauláná Arshad-ud-Din, who unwittingly trespassed on the game-preserves of Tughlugh.

Tughlugh had ordered the cleric before him and demanded to know the reason for the cleric's interference with his hunting.

The cleric answered that he wasn't aware that he was trespassing.

At this point, Tughlugh noticed that the cleric was Persian, and Tughlugh said that "a dog was worth more than a Persian."

The cleric responded, "Yes, if we had not the true faith, we should indeed be worse than dogs."

Puzzled, Tughlugh ordered the cleric to explain the "true faith"; thus was Tughlugh taught the doctrines of Islam, whose concepts of ummah, ghazat (holy war), and jihad inspire his territorial expansionism into Transoxiana.

Thereafter, Tughlugh had embraced Islam.

The conversion is also politically convenient in that he brands the dissident princes which he kills as "heathens and idolaters".

This act results in the amirs of Moghulistan doing the same, although the general population of the region is slower in converting.

The Chagatai Khanate had split in 1348 into two parts, western and eastern (Moghulistan).

The western half (Transoxonia and further west) of the Chagatai Khanate had by 1369 been conquered by Timur in his attempt to reconstruct the Mongol Empire.

The eastern half, mostly under what is now Xinjiang, remains under Chagatai princes.

Dawachi and the Khoit-Oirat prince Amursana had competed in 1752 for the title of Khan of the Dzungars, a confederation of several Tibetan Buddhist Oirat tribes that had emerged suddenly in the early seventeenth century.

The Qing dynasty has gone to war against the Dzungars, who live in the area stretching from the west end of the Great Wall of China to present-day eastern Kazakhstan and from present-day northern Kyrgyzstan to southern Siberia (most of which is located in present-day Xinjiang).

They are the last nomadic empire to threaten China, which they have done from the early seventeenth century.

Amursana had suffered several defeats at the hands of Dawachi and was thus forced to flee with his small army to the protection of the Qing imperial court.

The Yongzheng Emperor's successor, the Qianlong Emperor, has pledged his to support Amursana, who recognizes Qing authority; among those who support Amursana and the Chinese are the Khoja brothers Burhān al-Dīn and Khwāja-i Jahān.

Khan Khoja is kept as hostage whereas Burhan-ud-din is sent with Oirat, Chinese and Turks to re-conquer the Altishah, the six oasis towns along the rim of the Tarim Basin.

Qianlong in 1755 sends the Manchu general Zhaohui, who is aided by Amursana, Burhān al-Dīn and Khwāja-i Jahān, to lead a campaign against the Dzungars.

After several skirmishes and small scale battles along the Ili River, the Qing army led by Zhaohui approaches Ili (Gulja; modern Yining City) and forces Dawachi to surrender.

Qianlong appoints Amursana as the Khan of Khoid and one of four equal khans—much to the displeasure of Amursana, who had wanted to be the Khan of the Dzungars.

Amursana, still demanding to be khan of all Oirats, has allied the majority of the remaining Oirats and launched his rebellion against the Qing.

The Chinese armies had by now withdrawn leaving behind only a skeleton force under Ban Di.

Helpless and unable to do anything, Ban Di had committed suicide on October 4, 1755.

For the past eight months, Amursana has been the sole leader of the Oirats and the de facto Dzungar Khan.

Qianlong, as he had promised, has meanwhile appointed Khans for each of the four Oirat clans in a move designed to prevent them joining the rebellion.

Qing troops are once more dispatched in late March, 1756, and retake Ili.

Amursana escapes and flees to the Kazakh Khanate where his father-in-law, Ablai Khan, refuses to hand him over, despite the threat of a Qing invasion of his territory.

Qianlong rails at his generals for their failure to capture the fugitive, saying they are a waste of time and money.

He dismisses them and orders the withdrawal of all troops, then appoints Zhao Hui  commander of a small expeditionary force that is sent to garrison Ili.

Amursana returns to Ili to rally the insurgents and almost annihilates Zhao Hui's forces.

The hopelessly outnumbered Chinese general, despite putting up a spirited defense, is forced to retreat with five hundred soldiers.

The rebels cut the post routes to the capital but...

Qianlong, after the victory at Lake Khövsgöl, dispatches additional forces to Ili where they quickly rout the rebels.

Qing China recovers the Kuldja region through lengthy diplomatic negotiations in 1881 that end in the Treaty of Saint Petersburg..