Yaqub succeeded his father Yousuf Shah Chak, under warlike conditions, after Kashmir was invaded by the Mughal forces in late 1585.
[8] His grandfather, Ali Shah Chak married him to Sankar Devi, the daughter of Raja Bahadur Singh of Kishtwar.
[12] Yaqub was utterly unhappy after Akbar's hostile attitude towards him, calling him wicked and mad and giving him a meager allowance of only thirty to forty rupees.
[13] Yousuf, worried with the fear of Mughal advancement, was furious over Yaqub's action and wanted to imprison and punish him but was forcibly stopped by his ministers.
[19] Even though the clash went in the favour of Kashmiris,[20] Yousuf was convinced that he wouldn't be able to fend off Mughal invaders from the valley as hinted by Bhagwant Das.
[21] On 14 February 1586, Yousuf fled Kashmir and joined Bhagwant Das in the Mughal camp[22] leaving all the internal and external matters of the state in the hands of his naive and inexperienced son, Yaqub.
[27] As the Mughal forces suffered in heavy snowfall and the scarcity of food and resources, Kashmiri commanders inflicted great loss upon the invaders.
Seeing the disintegration of his forces, Bhagwant Das started to make peace talks with Sultan Yaqub by sending Mirza Akbar Shahi to him.
[43] After repelling the Mughal forces, Yakub neglected the advice of his ministers and counsellors[44] and despite warnings left the routes entering Kashmir undefended.
[47] Along the journey, Malik Hasan suggested that the monsoon season was going to commence, so they should rather attack and occupy Srinagar themselves as Yaqub was away on an administrative tour.
[52][40] Yaqub held Qazi Musa accountable for the recent rebellion and, after he refused to compute Caliph Ali's name in the public prayers, ordered his execution.
Yaqub also retired Muhammad Bhat off his position and imprisoned him, appointing Nazuk Dar, who was incapable and inexperienced in handling the external and internal affairs.
[43] These were one of the many reasons for Mughal annexation of Kashmir[42] as Yaqub's intolerance and harshness made Sunni pirs like Baba Daud Khaki to move away from the valley to Multan and other places.
Shaykh Yaqub Sarfi, a cousin of Baba Daud Khaki, proceeded to the court of Akbar and requested him to invade and annex Kashmir under a favourable agreement.
With this victory, the Mughals under Yadgar Hussain entered Srinagar on 14 October 1586 and had the Khutba read in the name of Emperor Akbar,[9] thus ending the short-lived Chak Sultanate.
[9] Yaqub set out from Kishtwar with a small following and to regain his throne and Sultanate from the Mughals, he established himself at Chanderkot with Abul Ma'ali.
[9] The three Chak chiefs adopted the guerrilla tactics and started to confront the Mughals in surprise attacks and cut down their resources.
[72] This greatly encouraged Yaqub, who attacked the west side of the city and set many houses at fire, including the palace in which Qasim Khan was residing.
[74] Yaqub lost his distinction in front of the Kashmiri forces after he ordered the execution of Husain Chak, who was one of the main contenders for the throne and was even appointed as Sultan by his supporters.
[77] Fighting ceased for two months as winter approached and in late 1587, Yaqub returned from Kishtwar and camped in a hill in the Vular Pargana (Pulwama).
The Kashmiris were again close to leading the battle in their favour but unfortunately for them, Yaqub's sipahsalar (commander-in-chief) was killed by an arrow that pierced his eye.
Akbar, after seeing the deteriorating circumstances in the Mughal's authority in Kashmir, replaced Qasim Khan with Yusuf Rizvi,[81] a Sayyid commander from Mashhad,Iran.
Yusuf Rizvi set out from Lahore along with Baba Khalil, Talib Isfahani and Muhammad Bhat, who had surrendered to the Mughals earlier, as guides in the middle of 1588.
[87] Yaqub returned from Kishtwar and settled in Panjyari, Dechhin Khawarah near Baramulla,[88] while Shams Chak established himself in the hills of Kamraj (Anantnag).
[89] Yaqub was determined that even if the Kashmiri army is disintegrated by the Mughal domination, the spirit to fend off foreign invasions and to protect the motherland should not be diminshed in any circumstances.
[90] After taking command and establishing the Mughal bureaus throughout Kashmir, Yusuf Rizvi sent Muhammad Bhat and Haji Miraki against Yaqub.
[90] Yaqub defeated the advance-guard led by Muhammad Mir, but both sides had to stop their advancements as heavy rain interfered.
[93][94] This, even though he had his morale and spirit high, immensely saddened and disheartened Yaqub deep down inside and so decided to give up the struggle for independence and surrender to the Mughals.
[104] Yaqub is also regarded as a symbol of independence among Kashmiris as he led a rebellion against Akbar and his occupying forces[105] and never let the misconduction of his disloyal and unfaithful commanders and soldiers affect his morale.