Therefore, his reign (1672–1686) is one of regents and ministers and was marked by chronic civil war among factious nobles, independence of provincial governors, paralysis of the central administration, Mughal invasions, secret alliances but pretend hostilities with the Maratha Empire and other neighbors, and the final absorption of Bijapur into the Mughal Empire in 1686. The prestige of Bijapur was so seriously damaged by internal disruptions that the Mughal General Diler Khan almost coerced and humiliated Sikandar. Despite several sacrifices and desperate attempts on the part of Sikandar, he could not satisfy the growing greed of the Mughals.
At last, Emperor Aurangzeb himself marched out in 1685 with a large army to fulfill the ambition of his life.
On 12 September 1686, Bijapur was occupied, its garrison surrendered and Bijapur Fort was annexed by the Mughal Empire. Sikandar Adil Shah was captured bound in silver chains and brought before the Mughal Emperor Aurangzeb, to whom he bowed three times.
The Adil Shahi dynasty thus came to an education