Timur's appointed successor Pir Muhammad was quickly cast aside, and Khalil gained control of Samarkand.

Khalil also gained an ally, Sultan Husayn Tayichiud, who had previously also made claims to the throne as a grandson of Timur.

The latter had considerable influence over Khalil, convincing him to appoint people of so-called low birth to high positions at the expense of the nobility.

He decided to return to the Ferghana Valley with his former mentor, Khudaidad Hussain, who went to Moghulistan (the realm of the eastern Chagatai Khans) in an attempt to win their support.

[3] However, Persian historian Khwandamir instead claims that Khudaidad Hussain began a civil war against Khalil and took him prisoner, delivering him along with his territory to eastern Chagatai Khan Shams-i-Jahan (r. 1399–1408).