Sikandar Sur had retired to the Siwalik Hills and Bairam Khan sent his forces there. The former shut himself in the hill-fortress of Mankot. The fort was besieged and the siege continued for six months. Sikandar Sur sued for peace. He surrendered the fort. He was given a Jagir and his son was otherwise provided.
In 1557, Muhammad Shah Adali died as a result of his conflict with the ruler of Bengal. Thus, another antagonist of Akbar was disposed of without any effort on his part.
Bairam Khan was a native of Badakshan and professed the Shia faith. He served faithfully both Humayun and Akbar. He fought in the Battle of Kanauj in 1540 and was taken a prisoner. However, he managed to escape and joined Humayun in his wanderings. He accompanied him to Persia and there exercised his won influence to get for Humanyun the support of the ruler of that country. He was with Humayun when the latter conquered Kabul, Khandhar and later on the Punjab, Delhi and Agra  . He was affectionately called Khani-baba (Lord Father).
It has already been pointed out that when Humayun died, Bairam Khan and Akbar were in the Punjab pursuing Sikandar Sur who was still not crushed. Akbar, a young man of 14, was in a very difficult situation. His followers advised him to retire to Kabul and from there attempt once again the conquest of India.
However, it was Bairam Khan who opposed the idea and insisted upon giving battle to Hemu who had already occupied Agra and Delhi. The credit of winning the Second Battle of Panipat goes in a large measure to Bairam Khan. He may be accused of the execution of Tardi Beg but expediency required such an action to strike terror into the hearts of the traitors and cowards amongst the Mughal officials.  He was also responsible for the execution of Hemu and his father.
After, The Battle of Panipat, Bairam Khan, by virtue of his wisdom, age and experience, was able to acquire considerable influence over Akbar and became virtually the ruler of the country (1556-60). In this position, he continued the work of conquest. He conquered Gwalior and Jaunpur but failed in the case of Ranthambore. He also did not succeed in his designs on Malwa.
However, Bairam Khan did not remain in power for long. He fell in 1560 and his fall was due to many causes. He appointed Sheikh Gadai as Sadr-i-Sadur. As the Sheikh was a Shia, his appointment was resented by the Sunni Muslims who were in a majority in India. The Sheikh was exempted from the ceremony of homage. He was given precedence over the Ulma and the Sayyids. He was given the authority to endorse the decrees with his seal. All this created a lot of heart-burning. Sheikh Gadai became the target of attack.
Bairam Khan showered favours on his friends and followers. The titles of Su’tan and Khan were given by him to his own servants and this was resented by the Muslim Nobility. The title of Panchhazari was given by him to his own favourites and the claims of others were not considered. He adopted a discriminatory attitude in the punishment of the offenders. He severely dealt with the servants of the royal houseold but let off the servants of his own household. He ordered the execution of the elephant-driver of Akbar without any cause.
There was also a suspicion that Bairam Khan was plotting to place on the throne Abdul Qasim, a son of Kamran. This was considered to be the height of disloyalty which could not be ignored. Bairam Khan was a Shia and his authority was resented by the Mughal nobles who were all Sunnis. They would like to pull him down from his high position. The execution of Tardi Beg created the feeling that Bairam Khan would not mind disposing of any noble, howsoever high he may be. This created a feeeling of awe and terror in their minds and their personal safety demanded the removal of Bairam Khan.
Bairam Khan did not try to win over the nobles of the court. On the other han ‘ he was thoroughly unpopular. “His disposition was arbitrary, haughty and jealous and he co, Id not easily tolerate the presence of possible rivals near his young master.”
As Akbar began to grow in years, he made up his mind to take over the administration into his own hands. Bairam Khan did not seem to like the idea and did not behave in a proper way This made Akbar impatient.’ There were also palace intrigues. Hamida Banu, the Mother of Akbar, Maham Anaga, Adham Khan and Shahad-ud-Din, Governor of Delhi, hated Bairam Khan and plotted to remove him. A conspiracy was hatched. Akbar went to Delhi to see his mother who was reported to be ill. It was at Delhi that Akbar wrote to Bairam Khan that he had decided to take into his own hands the reigns of the government, and, therefore, the latter should retire to Mecca’. He also offered him a Jagir for his maintenance.
Although Bairam Khan was advised by his followers to revolt, he refused to do so and submitted. Unfortunately, Pir Muhammad, a person whom Bairam Khan detested, was sent to hasten the departure of Bairam Khan from India to Mecca. This was not liked by Bairam Khan and he revolted. However, he was defeated and he begged forgiveness.
That was generously given by Akbar who received him “with the most princely grace and presented him with a splendid robne of honour.” Bairam Khan was allowed to proceed to Mecca with dignity. Unfortunately, he was murdered by an Afghan in Gujarat. His camp was plundered but his young son, Abdur Rahim, was saved. Later on, he rose to the position of Khan-i-Khanan and married a daughter of Prince Daniyal.
Dr. V. A. Smith has made the following observations on Bairam Khan: “The story of the transactions leading up the fall and death of Bairam Khan leaves an unpleasant taste. It seems to be clear that the intriguers who surrounded and controlled the young Padshah were resolved to get rid of the Protestor at any cost, and that they deliberately forced him into rebellion in order to ensure his destruction.
For a long time he steadily resisted the advice of Shaikh Gadai and others who counselled open opposition, and if his enemies had abstained from the outrage of deputing Pir Muhammad to pack him off as quickly as possible to Mecca, he would apparently have submitted to his Sovereign’s will, as his modern representative, Bismarck, submitted to William II, that is to say reluctantly, but as a matter of both necessity and duty. Bairam Khan obviously was only a half-hearted rebel, and was glad to be captured.
Even Abul Fazl, who made the most of the Protector’s faults, and could hardly find language emphatic enough to express his sense of the alleged merits of Maham Anaga and Pir Muhammad, was constrained to admit that ‘Bairam Khan was in reality a good man, and of excellent qualities.’ The court chronicle ascribes his deviations from the narrow path of rectitude to his association with evil advisers and his inordinate appetite for flattery.
As a matter of fact, Bairam Khan, although misled sometimes by his Maham Anaga chose hers during her brief tenure of power. He had never needed to punish the traitor Tardi Beg, and so to save his master’s cause. It is true that he made a mistake in giving his confidence at first to Pir Muhammad, but when discovered the man’s ingratitude and baseness, he had no hesitation in dismissing him.”
“Both Humayun and Akbar owed their recovery of the throne to Bairam Khan, and the obligations of gratitude required that when the time came for Akbar to take the reins into his own hands the demission of his faithful charioteer should be effected as gently as possible.
But the many enemies of Bairam Khan were not in a honour to make his exit easy. If they could have had their way unobstructed; they would certainly have put him to death. The generosity of his receptic t after the failure of his rebellion may be fairly attributed to young Akbar himself, who had little to do with the previous transactions, for which Maham Anaga was responsible , as her panegyrist Abul Fazl expressly affirms  .”
According to Sir Wolseley Haig, “It was chiefly due to Bairam that Akbar owed his throne. It was inevitable that a youngman of Akbar’s force of character should emerge from a state of tutelage, but he would have done well to wait, for he was not yet fit to assume the sole charge of his empire and remained for four years more under the pernicious influence of the harem party.
The means by which he escaped from Bairam’s influence were probably the best which he could have adopted but the insults and ungenerous treatment which drove the protector into rebellion would be a blot upon his memory were it not certain that they originated with Bairam’s bitterest enemy in the harem party.”
About Bairam Khan, Dr. A. L. Srivastava observes thus: “Besides being a good soldier and commander and a very able administrator, Bairam Khan was endowed with a talent for scholarship and love of poetry. Humayun owed the recovery of his Indian dominion to him and Akbar his throne and the outline of administrative structure of his kingdom. He was a liberal patron of scholars and is said to have bestowed on three eminent men of letters and art, namely, Hashmi Qandhari, Ram Das of Lucknow and Hijaz Khan Badayuni, one lakh of tanka each.
The estimate of his character by the contemporary critical historian, Abdul Qadir Badayuni, who was a bigoted Sunni and hardly ever saw any good in a Shia, deserves to be quoted. ‘In wisdom, generosity, sincerity, goodness of disposition, submissiveness and humility’, writes he, he (Bairam Khan surpassed all. He was a friend to religious mendicants (Dervishes), and was himself a deeply religious and well-intentioned man. The second conquest of Hindustan and the building up of the empire were due to his strenuous efforts, his valour and his statesmanship.”
“He was driven into rebellion against his will, and was glad to submit to his sovereign. Akbar deserves credit for according him a very generous treatment in view of his long and meritorious services.” 
Iqtidar Alam Khan says that “The struggle between Bairam Khan and his opponents at the court was basically a struggle between the central authority as represented by the Regent and the rest of the nobles. The king during this period was simply a figure-head whose whims and fancies led him frequently into becoming a tool in the hands of the elements working against the Regent.
While Bairam Khan endeavoured to establish a unified command and weld together the two main elements constituting the Mughal nobility (the Chaghtais and the Khurasanis) into one whole, the bulk of the nobility looked askance at all such attempts on his part and took these as deliberate assaults on their freedom of action in their own commands and charges. Bairam Khan’s measures implied a certain amount of curtailment of the nobles powers and freedom of action. Even such nobles as were close to Bairam Khan often found themselves pitted against the central authority.
Bairam Khan’s dilemma was that on the one hand he wanted to curtail the independence and autonomy of the nobles and on the other, he had to depend for his power and authority on one or another section of the nobility. It was not possible to introduce my new element into the Mughal nobility for counter-balancing the existing factions at that early stage when the process of the re-establishment of the empire in India was not yet complete.
It was not feasible to recruit the Afghan chiefs in the nobility as they were the enemies of the Mughals. It is possible that Bairam Khan might have thought in terms of using the recruits from amongst the Rajput chiefs for counter-balancing the influence of the existing factions. Even if he wanted to do so, that would have taken a long time to materialise, but the problem facing him demanded an immediate solution. The only way open to him was either to placate his opponents by giving them sweeping concessions one after another or adopt a stern attitude towards them.
A recourse to the first alternative led to the compromise of April 1558 A.D. which practically paralysed the central authority. When to retrieve the situation, Bairam Khan made a frontal attack upon his opponents, he found himself in complete isolation which led to his overthrow.
The crisis leading to Bairam Khan’s exist was perhaps the first round of the struggle between the central authority and forces operating in the opposite direction within the Mughal polity. It resulted in the victory for the latter trend. That explains why Akbar had to face such enormous difficulties in his relations with the nobility between 1562 and 1567 after his full assumption of sovereign powers.”