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Strife with Sher Shah Suri

Shortly after Humayun had marched on Gujarat, Sher Shah Suri saw an opportunity to wrest control of Agra from the Mughals. He began to gather his army together hoping for a rapid and decisive siege of the Mughal capital. Upon hearing this alarming news, Humayun quickly marched his troops back to Agra allowing Bahadur to easily regain control of the territories Humayun had recently taken. In February 1537, however, Bahadur was killed when a botched plan to kidnap the Portuguese viceroy ended in a fire-fight that the Sultan lost. Bahadur's passing caused a power vacuum in Gujarat, which ultimately paved the way for the Mughals to become the region's dominant force.

While Humayun succeeded in protecting Agra from Sher Shah, the second city of the Empire, Gaur the capital of the vilayat of Bengal, was sacked. Humayun's troops had been delayed while trying to take Chunar, a fort occupied by Sher Shah's son, in order to protect his troops from an attack from the rear. The stores of grain at Gauri, the largest in the empire, were emptied, and Humayun arrived to see corpses littering the roads. The vast wealth of Bengal was depleted and brought East, giving Sher Shah a substantial war chest.

Sher Shah withdrew to the east, but Humayun did not follow: instead he "shut himself up for a considerable time in his Harem, and indulged himself in every kind of luxury". Hindal, Humayun's 19-year-old brother, had agreed to aid him in this battle and protect the rear from attack, but he abandoned his position and withdrew to Agra, where he decreed himself acting emperor. When Humayun sent the grand Mufti, Sheikh Buhlul, to reason with him; the Sheikh was killed. Further provoking the rebellion, Hindal ordered that the Khutba, or sermon, in the main mosque be surrounded.

Humayun's other brother, Kamran Mirza, marched from his territories in the Punjab, ostensibly to aid Humayun. However, his return home had treacherous motives as he intended to stake a claim for Humayun's apparently collapsing empire. He brokered a deal with Hindal providing that his brother would cease all acts of disloyalty in return for a share in the new empire, which Kamran would create once Humayun was deposed.

In June 1539 Sher Shah met Humayun in the Battle of Chausa on the banks of the Ganges, near Buxar. This was to become an entrenched battle in which both sides spent a lot of time digging themselves into positions. The major part of the Mughal army, the artillery, was now immobile, and Humayun decided to engage in some diplomacy using Muhammad Aziz as ambassador. Humayun agreed to allow Sher Shah to rule over Bengal and Bihar, but only as provinces granted to him by his Emperor, Humayun, falling short of outright sovereignty. The two rulers also struck a bargain in order to save face: Humayun's troops would charge those of Sher Shah whose forces then retreat in feigned fear. Thus honour would, supposedly, be satisfied.

Once the Army of Humayun had made its charge and Sher Shah's troops made their agreed-upon retreat, the Mughal troops relaxed their defensive preparations and returned to their entrenchments without posting a proper guard. Observing the Mughals' vulnerability, Sher Shah reneged on his earlier agreement. That very night, his army approached the Mughal camp and finding the Mughal troops unprepared with a majority asleep, they advanced and killed most of them. The Emperor survived by swimming across the Ganges using an air-filled "water skin", and quietly returned to Agra. Humayun was assisted across the Ganges by Shams al-Din Muhammad.