Edited with new, less confusing, description of the timeline:



Li Zicheng takes Beijing in 1644 and kills the Chongzhen Emperor as IOTL, but is defeated and killed at Shanhai Pass by the Manchu. Zhang Xianzhong, warlord in control of Sichuan, builds an agricultural and administrative base in the province during this time and raises an army. When Li is defeated, he marches rapidly along the north China plain to fill the vacuum. A Later Jin army under Prince Dorgon attempts to march south but is thwarted west of Qufu by Zhang's army, now consisting also of Ming and Shun defectors. This takes heavy casualties and cannot pursue the Later Jin into Zhili, but the Manchu flee and regroup after the defeat.



Following this, Zhang declares himself Emperor of Great Shu, after his state and the province he ruthlessly ruled, while the Manchu fought a civil war between Hooge and the Shunzhi Emperor's traditionalists (loyal to dead Emperor Wen [Hong Taiji]) and Karma Kagyu Buddhists under the Vajrayana Emperor Wu. Hooge would be defeated by Ligdan Khan's Gelug Buddhist confederacy of Mongol nations, and eventually lose the civil war. Emperor Wu would build fortifications with newer artillery on the borders in Zhili, south of what had been Beijing. The city would be made the capital by Emperor Wu, renamed Nandu. Zhang would make his capital Luoyang.



After Gushi Khan's son Tashi Batur rebelled in Qinghai under the banner of the Karma Kagyu school of Vajrayana Buddhism, he and his sect were ruthlessly wiped out by the Khoshud Khan with the help of Ligdan Khan, who under the influence of his Oirat councillor Badma Erdeni had united most of the Eastern Mongols under Gelug. The cities of Moghulistan and the Gansu Corridor, as well as most of the Western Mongols and Oirat, would be brought under their control in the 1640s.



Gushi Khan of the Khoshud unites the Eastern Mongols behind the 5th Dalai Lama and the Gelug sect after defeating a Karma Kagyu revolt led by his son with the help of fellow-Gelug Ligdan Khan of the Later Yuan Chakhar Confederacy. The Later Yuan had reunited the Eastern and Western Mongols with the help of Ming funds and weapons and Gelug Buddhist Manchu fleeing the anti-Gelug reprisals of the Karma Kagyu Buddhist Emperor Wu of Later Jin, who had won the civil war.



Zhang made himself emperor after the defeat of the Later Jin southern expedition, declaring the Jiantong reign. His campaigns in the north against the Later Jin drained the treasury, while his Chancellor Wang's policy of seizing assets of monasteries in order to pay for them caused widespread resentment. The campaigns in Zhili resulted in high casualties and little progress as Emperor Wu had built fortifications armed with newer artillery, and Zhang spent even more money procuring the loyalty of a rebel admiral of Taiwan's Zheng family (protectors of the Hongguang Emperor of Ming), only to lose these substantial naval forces to Manchu artillery and Korean forces in an assault on Later Jin coastal fortifications.



In a bloody battle outside of Nandu (Beijing), the Jiantong Emperor was killed. The army, threatening to disperse, was exhorted by a popular officer to stay together and garrison the northern forts of Shu in order to protect the country from the Manchu. This general, Feng Shuangli, made himself King of Xue and resisted the Later Jin successfully when they attacked north China alongside the Wan.



When Western Chinese Buddhists launched an uprising led by a group of radical Vajrayana millenarians, the regency of the ten year old Dingxi Emperor were unable to hold the country together and allowed Xi'an to be taken by rebels. This signaled the weakness of Shu to Gushi Khan and the forces of the Tibetans and Chakhar joined together in a grand council to acclaim the Dalai Lama the Arhat Emperor of Great Wan (大卍) before launching a massively successful campaign of conquest across China, destroying the remnants of Great Shu as well as the Great Xue and much of the Southern Ming.



Part of a DBWI I participated in