Since Akbar held the throne at his teen age; he had been supported by a group of nobles.
Bairam Khan remained at the helm of affairs of the Mughal Empire for almost next four years and during this period, he kept the nobility fully under control.
The territories of the Mughal Empire were extended from Kabul (in the north) to Jaunpur (in the east) and Ajmer (in the west).
Mughal forces captured Gwalior and vigorous efforts were made to conquer Ranthambhor and Malwa.
Over a period of time, Akbar was approaching the age of maturity. On the other hand, Bairam Khan became arrogant and had offended many powerful persons and nobles of Mughal court (as he held supreme power). Many of the nobles complained to Akbar that Bairam Khan was a Shia, and that he was appointing his own supporters and Shias to high offices, while neglecting the old nobles.
The charges against Bairam Khan were not much serious in themselves, but he (Bairam Khan) became egoistical, and hence failed to realize that Akbar was growing up. In fact, there was friction on a petty matter, which made Akbar realize that he could not leave the state affairs in someone else's hands for any more.
To control Bairam Khan, Akbar played his cards cleverly. He left Agra on the pretext of hunting, and came Delhi. From Delhi, Akbar issued a farman (summon) dismissed Bairam Khan from his office, and ordered all the nobles to come and submit to him personally.
The farman made Bairam Khan realize that Akbar wanted to take power in his own hands; so, he was prepared to submit, but his opponents were keen to ruin him. They heaped humiliation upon him until he was goaded to rebel.
The rebellion distracted the empire for almost six months. Finally, Bairam Khan was forced to submit in Akbar’s court; Akbar received him cordially, and gave him the option of serving at the court (anywhere), or retiring to Mecca.
Bairam Khan chose to retire to Mecca. On his way to Mecca, he was assassinated at Patan near Ahmadabad by an Afghan who bore him a personal grudge.
Bairam Khan's wife and a young child were brought to Akbar at Agra. Akbar married Bairam Khan's widow (who was also his cousin), and brought up the child as his own son.
Bairam Khan’s child later became popular as Abdur Rahim Khan-i-Khanan and held some of the most significant offices and commands in the Mughal Empire.
During Bairam Khan's rebellion, some groups and individuals in the nobility became politically active. The group included Akbar's foster-mother, Maham Anaga, and her relatives. However, Maham Anaga soon withdrew from politics.
Maham Anaga’s son, Adham Khan, was an impetuous young man. He assumed independent airs when he had been sent to command an expedition against Malwa. He claimed the post of the wazir, and when this was not accepted, he stabbed the acting wazir in his office. His tyrannical act enraged Akbar. In 1561, Adham Khan had been thrown down from the parapet of the fort and he died.
Much before Akbar’s maturity and establishing his full authority, the Uzbeks formed a powerful group. They held important positions in eastern Uttar Pradesh, Bihar, and Malwa.
Between the period of 1561 and 1567, the Uzbeks rebelled many times, forced Akbar to take the field against them. Every time Akbar was induced to pardon them. However, 1565 rebel exasperated Akbar at such a level that he vowed to make Jaunpur his capital till he had rooted them out.
Encouraged by Uzbeks’ rebellions, Akbar's half-brother, Mirza Hakim, who had seized control of Kabul, advanced into Punjab, and besieged Lahore. As a result of this, the Uzbek rebels formally proclaimed him as their ruler.
Mirza Hamim’s attack was the most serious crisis Akbar had to face since Hemu's capture of Delhi. However, Akbar's bravery and a certain amount of luck enabled him to triumph.
From Jaunpur, Akbar directly moved to Lahore, forced Mirza Hakim to retire. Meanwhile, the rebellion of the Mirza’s was crushed, the Mirzas fled to Malwa and thence to Gujarat.
In 1567, Akbar returned back to Jaunpur from Lahore. Crossing the river Yamuna nearby Allahabad (at the peak of the rainy season), Akbar surprised the rebels led by the Uzbek nobles and completely routed them out.
The Uzbek leaders were killed in the battle; likewise, their protracted rebellion came to an end.