Ayub suffered a number of setbacks in 1968. He was almost assassinated at a ceremony marking ten years of his rule. Riots followed, and Bhutto was arrested as the instigator. At Dhaka a tribunal that inquired into the activities of the already-interned Mujib was arousing strong popular resentment against Ayub. A conference of opposition leaders and the cancellation of the state of emergency (in effect since 1965) came too late to conciliate the opposition. A state of near anarchy reigned with protests and strikes throughout the country. The police appeared helpless to control the mob violence, and the military stood aloof. At length, on March 25 Ayub resigned and handed over the administration to the commander in chief, General Agha Mohammad Yahya Khan.

Once again the country was placed under martial law. Yahya assumed the titles of chief martial law administrator and president. He announced that he considered himself to be a transitional leader whose task would be to restore order and to conduct free elections for a new constituent assembly, which would then draft a new constitution. He appointed a largely civilian cabinet in August 1969 in preparation for the election, which was scheduled to take place in December 1970. Yahya moved with dispatch to settle two contentious issues by decree: the unpopular "One Unit" of West Pakistan, which was created as a condition for the 1956 constitution, was ended; and East Pakistan was awarded 162 seats out of the 300-member National Assembly.

On November 12, 1970, a cyclone devastated an area of almost 8,000 square kilometers of East Pakistan's mid-coastal lowlands and its outlying islands in the Bay of Bengal. It was perhaps the worst natural disaster of the area in centuries. As many as 250,000 lives were lost.

Two days after the cyclone hit, Yahya arrived in Dhaka after a trip to Beijing, but he left a day later. His seeming indifference to the plight of Bengali victims caused a great deal of animosity. Opposition newspapers in Dhaka accused the Pakistani government of impeding the efforts of international relief agencies and of "gross neglect, callous inattention, and bitter indifference."

Mujib, who had been released from prison, lamented that "West Pakistan has a bumper wheat crop, but the first shipment of food grain to reach us is from abroad" and "that the textile merchants have not given a yard of cloth for our shrouds." "We have a large army," Mujib continued," but it is left to the British Marines to bury our dead." In an unveiled threat to the unity of Pakistan he added, "the feeling now pervades . . . every village, home, and slum that we must rule ourselves. We must make the decisions that matter. We will no longer suffer arbitrary rule by bureaucrats, capitalists, and feudal interests of West Pakistan."