Second military era (1977-1988)

Pakistan had been a US ally for much of the Cold War, from the 1950s and as a member of CENTO and SEATO. The Soviet invasion of Afghanistan renewed and deepened the US-Pakistan alliance. The Reagan administration in the United States helped supply and finance an anti-Soviet insurgency in Afghanistan, using Pakistan as a conduit. In retaliation, the Afghan secret police, KHAD, carried out a large number of terrorist operations against Pakistan, which also suffered from an influx of illegal weapons and drugs from Afghanistan. In the 1980s, as the front-line state in the anti-Soviet struggle, Pakistan received substantial aid from the United States as it took in millions of Afghan (mostly Pashtun) refugees fleeing the Soviet occupation. The influx of so many refugees - the largest refugee population in the world- had a heavy impact on Pakistan and its effects continue to this day. General Zia's martial-law administration gradually reversed the socialist policies of the previous government, and also introduced strict Islamic law in 1978, often cited as the contributing factor in the present climate of sectarianism and religious fundamentalism in Pakistan. Ordinance XX was introduced to limit the freedom of the Ahmadis to call themselves Muslims in Pakistan. Further, in his time, secessionist uprisings in Balochistan were put down violently but successfully by the provincial governor, General Rahimuddin Khan.

General Zia lifted martial law in 1985, holding non-partisan elections and handpicking Muhammad Khan Junejo to be the new Prime Minister, who readily extended Zia's term as Chief of Army Staff until 1990. Junejo however gradually fell out with Zia as his administrative independence grew; for example, Junejo signed the Geneva Accord, which Zia greatly frowned upon. After a large-scale blast at a munitions dump in Ojhri, Junejo vowed to bring to justice those responsible for the significant damage caused, implicating several senior generals. Zia dismissed the Junejo government on several charges in May 1988 and called for elections in November 1988. However, General Zia died in a plane crash on August 17 1988.