After the withdrawal of the Mughals, Bahadur was declared Sultan. Muhammad Khan was appointed minister. Miyan Muhammad was, however, unhappy at the turn of events. He still wanted to push forward the claims of his protege Ahmad to the throne.
Chand Bibi had to seek the help of his nephew Ibrahim Adil Shah who asked Miyan Manju to leave from Bijapur alongwith Ahmad where they were employed in the Imperial service.
Meanwhile fresh difficulties arose due to the high handed policies of Muhammad Khan. Chand Bibi again sought the help of Ibrahim Adil Shah who sent an army under Suhail Khan. Muhammad was besieged in the fort of Ahmadnagar for four months when he appealed to the Mughals for help. But the exasperated garrison handed him over to Chand Bibi.
Thus her internal troubles seemed to have been over but she had to face the Mughals. They were in occupation of some territories of Ahmadnagar including Pathri not ceded to them according to the last treaty. Moreover, they had captured two more fortresses Gawilgarh and Narnala of Berar.
The appeal of help from Muhammad Khan gave an opportunity to the Mughals to reopen the offensive. Her appeal to Bijapur and Golkonda brought a ready response. The allied forces advanced towards Berar and a fierce battle was fought between the contending armies at Sonpat on the banks of the river Godavari.
The Mughals came out victorious (A.D. 1597). The Mughals were also able to conquer Lohgarh, Mankar, Kherla, Nasik, Abugarh, Batiala, Taltam, etc. But their’ further progress was hampered due to acute differences between Prince Murad and Khan-i-Khanan.
The latter was replaced by Abdul Fazl. Prince Murad died soon afterward due to his intemperance and was replaced by Daniyal. The fort of Ahmadnagar was invested with renewed vigour.
Chand Bibi knew that the position was hopeless and therefore decided to hand over the fort to the Mughals on conditions of safe passage for the Sultan, herself and the garrison. She was suspected to be in league with the Mughals and a mob headed by the eunuch Jita Khan or Hamid Khan put her to death (July 1600).
Thus ended the life of that brave lady who had staked her life to save the honour of two kingdoms. She was a brave and valourous lady whose beauty, generosity and capabilities entitle her to rank with Raziah,
Nur Jahan and Ahilyr Bai. Radhey Shyam in his well known work “The kingdom of Ahmadnagar” pays her a well deserved tribute. “So great was the love she inspired that the peasants of the western hills refused for many years to believe that she was dead.
She has escaped, they said, through an underground passage and was hiding in some deep fold of the Syhadri Mountains. When the time will come, she would again reveal herself, drive the Mughals across the Vindhyas and bring once more the golden years of Ahmadnagar”.
With her death the garrison lost all zeal for resistance and surrendered to the Mughals in August, 1600. Ahmadnagar was annexed to Mughal Empire and the young Sultan Bahadur Nizam Shah was sent as a prisoner to Gwalior fort where he passed the rest of his life.
The capital and its adjoining areas no doubt became a part of the Mughal Empire but quite a substantial part of the kingdom remained in the hands of the Nizam Shahi nobles such as Malik Ambar and Raju Deccani who refused to owe allegiance to the Mughal king.
They carved independent principalities for themselves, and disbanded soldiers and officers of the different kingdom took service with them. Malik Ambar soon became “the spearhead of the movement which aimed at the expulsion of the Mughals from the Deccan.”