Politics: 1958–1972
By 1962, Ayub Khan introduced a new constitution and announced he would run in the next Presidential election. The opposition parties united under the Combined Opposition Party alliance and fielded a joint candidate against Ayub Khan in the Presidential elections. As an opposition leader, Wali Khan supported the consensus candidate Fatima Jinnah, sister of Pakistan's founder Muhammad Ali Jinnah. Wali Khan assisted Fatima Jinnah in her election campaign and served as her election agent.
The opposition's election campaign however proved a failure and Ayub Khan was re-elected in 1964, in part due to alleged vote rigging by the central government, and also because of divisions within the opposition. These divisions were particularly sharp between Wali Khan and National Awami Party President Maulana Bhashani, as the Pro-Mao Bhashani was alleged to have unofficially supported Ayub Khan because of the government's pro-China policy.
These divisions came to the surface in 1967, when the National Awami Party formally split into Wali Khan and Bhashani factions. Wali Khan was elected President of his own faction of the National Awami Party in June 1968. In the same year, popular unrest broke out against Ayub Khan's rule in Pakistan, due to increasing corruption and inflation. Wali Khan, along with most of the opposition parties, including future Bangladeshi President Sheikh Mujibur Rahman and others, formed the Democratic Action Committee to negotiate with Ayub Khan for the restoration of democracy.
Attempting to provide Ayub Khan with an honourable exit from power, negotiations between Ayub Khan and the opposition continued between 9 and 10 May 1969. However, despite a compromise agreement on some issues, it was alleged that the military leadership and its political allies did not want Ayub Khan to succeed. Wali Khan held a separate meeting with Ayub Khan on 11 May to convince him to compromise. Ayub refused, and shortly afterwards Ayub resigned under pressure from the military.
The new military leader, Yahya Khan, called for general and provincial elections in 1970, promising to transfer power to the majority party. In the elections, Sheikh Mujeeb-ur Rehman, Bengali nationalist and leader of the Awami League, won a majority of seats nationally and all the seats from the East wing of the country. (See Elections in Pakistan.) In West Pakistan, the charismatic populist Zulfiqar Ali Bhutto won the second largest number of seats in the assembly, almost solely from the Punjab and Sindh provinces. Wali Khan was elected to both the provincial Assembly as a member of the Provincial Assembly and the National Assembly from his home constituency of Charsadda.
Despite the results, the military government rejected the Awami League's victory. Shocked on hearing the news that the military junta would not transfer power to the majority Bengalis, Khan was to later tell A.P. journalist Zeitlin, "I remember Bhutto said that it had been arranged with the 'powers that are' that in East Pakistan Sheikh Mujibur Rahman would rule, and in West Pakistan, Mr. Bhutto would be the Prime Minister."
In 1971, in an attempt to avert a possible showdown between the Military and the people of East Pakistan, on 23 March 1971, Khan, along with other Pakistani politicians, jointly met Sheikh Mujibur Rahman. They offered support to Mujib in the formation of a government, but it was too late to break the impasse as Yahya Khan had already decided on a full-scale military crackdown. Pakistan's increasing vulnerability and widespread international outrage against the military crackdown eventually created a situation that led to war in East Pakistan. This war proved disastrous and culminated in Pakistan's armed forces being defeated in East Pakistan and the creation of the new state of Bangladesh. Shocked by the defeat, Yahya Khan resigned from office and the military. Under General Gul Hassan Khan, Zulfikar Ali Bhutto was brought back from America and appointed the Civilian Chief Marshal Law Administrator and President.
During the martial law crackdown against East Pakistan, the National Awami Party under Wali Khan was one of a handful of parties that protested the military operation. In one case, Khan helped a senior East Pakistani diplomat's son escape to Afghanistan from possible internment in West Pakistan. The military government, in retaliation against the protests, banned the party and launched mass arrests of party activists.