Mujib was one of the key leaders to rally opposition to President Ayub Khan's Basic Democracies plan, the imposition of martial law and the one-unit scheme, which centralised power and merged the provinces. Working with other political parties, he supported opposition candidate Fatima Jinnah against Ayub Khan in the 1964 election. Mujib was arrested two weeks before the election, charged with sedition and jailed for a year. In these years, there was rising discontent in East Pakistan over the atrocities committed by the Pakistani Armed Forces against Bengalis and the neglect of the issues and needs of East Pakistan by the ruling regime. Despite forming a majority of the population, the Bengalis were poorly represented in Pakistan's civil services, police and military. There were also conflicts between the allocation of revenues and taxation.
Unrest over continuing denial of democracy spread across Pakistan and Mujib intensified his opposition to the disbandment of provinces. In 1966, Mujib proclaimed a 6-point plan titled Our Charter of Survival at a national conference of opposition political parties at Lahore, in which he demanded self-government and considerable political, economic and defence autonomy for East Pakistan in a Pakistani federation with a weak central government.
According to his plan:
- The constitution should provide for a Federation of Pakistan in its true sense on the Lahore Resolution and the parliamentary form of government with supremacy of a legislature directly elected on the basis of universal adult franchise.
- The federal government should deal with only two subjects: defence and foreign affairs, and all other residuary subjects shall be vested in the federating states.
- Two separate, but freely convertible currencies for two wings should be introduced; or if this is not feasible, there should be one currency for the whole country, but effective constitutional provisions should be introduced to stop the flight of capital from East to West Pakistan. Furthermore, a separate banking reserve should be established and separate fiscal and monetary policy be adopted for East Pakistan.
- The power of taxation and revenue collection shall be vested in the federating units and the federal centre will have no such power. The federation will be entitled to a share in the state taxes to meet its expenditures.
- There should be two separate accounts for the foreign exchange earnings of the two wings; the foreign exchange requirements of the federal government should be met by the two wings equally or in a ratio to be fixed; indigenous products should move free of duty between the two wings, and the constitution should empower the units to establish trade links with foreign countries.
- East Pakistan should have a separate militia or paramilitary forces.
Mujib's points catalysed public support across East Pakistan, launching what some historians have termed the 6-point movement – recognised as the definitive gambit for autonomy and rights of Bengalis in Pakistan. Mujib obtained the broad support of Bengalis, including the Hindu and other religious communities in East Pakistan. However, his demands were considered radical in West Pakistan and interpreted as thinly veiled separatism. The proposals alienated West Pakistani people and politicians, as well as non-Bengalis and Muslim fundamentalists in East Pakistan.
Mujib was arrested by the army and after two years in jail, an official sedition trial in a military court opened. Widely known as the Agartala Conspiracy Case, Mujib and 34 Bengali military officers were accused by the government of colluding with Indian government agents in a scheme to divide Pakistan and threaten its unity, order and national security. The plot was alleged to have been planned in the city of Agartala, in the Indian state of Tripura. The outcry and unrest over Mujib's arrest and the charge of sedition against him destabilised East Pakistan amidst large protests and strikes. Various Bengali political and student groups added demands to address the issues of students, workers and the poor, forming a larger "11-point plan." The government caved to the mounting pressure, dropped the charged and unconditionally released Mujib. He returned to East Pakistan as a public hero.
Joining an all-parties conference convened by Ayub Khan in 1969, Mujib demanded the acceptance of his six points and the demands of other political parties and walked out following its rejection. On 5 December 1969 Mujib made a declaration at a public meeting held to observe the death anniversary of Suhrawardy that henceforth East Pakistan would be called "Bangladesh":
"There was a time when all efforts were made to erase the word "Bangla" from this land and its map. The existence of the word "Bangla" was found nowhere except in the term Bay of Bengal. I on behalf of Pakistan announce today that this land will be called "Bangladesh" instead of East Pakistan."
Mujib's declaration heightened tensions across the country. The West Pakistani politicians and the military began to see him as a separatist leader. His assertion of Bengali cultural and ethnic identity also re-defined the debate over regional autonomy. Many scholars and observers believed the Bengali agitation emphasised the rejection of the Two-Nation Theory – the case upon which Pakistan had been created – by asserting the ethno-cultural identity of Bengalis as a nation. Mujib was able to galvanise support throughout East Pakistan, which was home to a majority of the national population, thus making him one of the most powerful political figures in the Indian subcontinent. It was following his 6-point plan that Mujib was increasingly referred to by his supporters as "Bangabandhu" (literally meaning "Friend of Bengal" in Bengali).