The intervention of Cardinal Lavigerie was providential because the institutes of Comboni suffered a serious setback in Sudan. Bishop Comboni died in the first stages of the revolution of the religious and political leader Muhammad Ahmad al-Mahdi. On 29th June 1881, he proclaimed he was the expected Mahdi and urged his countrymen to join him as he rose in arms against the Turkish-Egyptian government of Sudan. While Comboni was dying, the Mahdi and his followers were heading for the Nuba Mountains, where the revolutionary movement attracted thousands of disaffected tribesmen. Here they annihilated two armies sent against them and, marauding across the plains of Cordofan, laid siege to the capital, al-Ubayyid, which they captured. In November 1883 they obliterated an Egyptian relieving force commanded by General W. Hicks. In the course of the campaign, the rebels overran the missions started by Comboni at El-Obeid, Dilling and the farming settlement at Malbes. The missionaries were taken prisoner and subject to terrible torture: the sisters were brutally flogged in an attempt to make them deny Christ and accept Islam. The missions of Khartoum, Berber, and Scellal had to be abandoned.
After the killing of Gordon Pasha, England sent a military force led by Lord Kitchener who defeated the Mahdi in September 1898; Khartoum and Omdurman were free and the missionaries of Comboni could return to their deserted missions.
In January 1894 the whole of southern Sudan and northern Uganda was returned to the Vicariate Apostolic of Central Africa and Mgr Roveggio was appointed Vicar Apostolic. After the defeat of the Mahdi he was able to take up his duties, based at Khartoum. He died of fever in Berber in 1902 and was replaced by Bishop Geyer. At this time, the establishment of missions further south and efforts to enter Uganda were impeded by the problems between Belgian and British authorities over the Lado Enclave.