The extremist sectarian intolerance came to Pakistan only after 1979 revolution in Iran. The Iranian revolution emboldened the Shiite Muslims of Pakistan against their suffering at the hands of anti-Shiite groups. This was further aggravated when a Sunni-dominated Iraq with the backing of the USA and Saudi Arabia waged a war upon Shiite dominated Iran.
The soviet Afghanistan War was the most critical event responsible for spreading militancy and intolerance in Pakistan. In order to fight proxy war against the Soviets, the US and the Arab countries provided the funds for serving The Mujahedeen who were motivated for battle through religious propaganda urging them to expel the infidels from Afghanistan.
The armed freedom struggle surfaced in Kashmir during the eighties gave the resistors a continued reason to be present in the region, which was exploited by Pakistan. Therefore after 9/11, when a ban was put on these fighters, they turned their guns towards their adopted country.