When the latter was again enthroned as Chagatai Khan in 1266, Baraq gained support among the army for a coup and deposed Mubarak Shah in September of that year.
In the next battle, however, Kaidu defeated Baraq near Khujand with the assistance of Mengu-Timur, the Khan of the Golden Horde who sent 3 tumens under his uncle Berkhe-Chir.
Peace was therefore proposed, and Baraq was pressured by the governors of the sedentary areas of the khanate, Mas'ud Beg and Daifu, to accept.
Neither side gained control of the cities; the direct administration of these instead devolved to Mas'ud Beg, while Baraq and Kaidu agreed to reside only in the deserts and mountains.
Baraq persuaded a Chaghadaid commander under the service of Abaqa, Tegüder, to revolt, and himself defeated the Ilkhan's forces in Khurasan.
Soon afterward, Qipchaq entered into an argument with Baraq's general Jalayirtai, and used this as an excuse to head back to Kaidu.
When Baraq's lieutenants had neutralized the rebels, he wrote that the assistance was no longer necessary, but Kaidu's force continued to approach, with the intention of destroying the power of the Chaghadaids.
Only a month later, Kaidu had himself crowned Khan and reserved the right to appoint the head of the Chagatai Khanate, a power he retained for the rest of his life.