He sought to subjugate it, but he did not succeed in most of his raids. Finally, he realized that it was time for independence.

He was appointed governor of Khartoum and buried there. Some officials asked him why he did not seek independence, even though he was the first to impose taxes on the people. The country was divided into two parts: one for properties and one for individuals.

The property taxes were specific to the lands north of Khartoum, while the individual taxes were specific to the rest of the Sudanese lands, as they agreed to it. He imposed an annual tax on nomadic tribes and appointed Ja'far Pasha Sadiq in his place. In the year 1884, the Fourth Sudanese Regiment revolted in the city of Kassala, killed their officers, looted the city, killed all the whites, and occupied the city's positions and surrounding forts. Their situation worsened, so the Khedive Ismail Pasha sent the late Ja'far Mudabir Pasha, along with Adam Pasha al-Sudani, to suppress the rebellion, capture them, and eradicate them.

The Khedive issued a decree prohibiting the formation of cavalry units from Sudanese soldiers, that they not be taught to fire cannons, that they not occupy strategic positions, and that no high-ranking officers emerge from them. After punishing the rebels, Ja'far Mudabir Pasha returned.

He was known for spreading knowledge among the people and raising the status of scholars, and he provided them with salaries. It is not surprising, for those who recognize merit know it. He was a man of piety. He left Khartoum with debts exceeding one thousand pounds, as his salary did not cover his needs due to his extensive spending on the poor and needy. Among his generous acts was that he used to invite more than a hundred people to dine at his luxurious table, most of them poor, for every lunch and dinner.