On November 3, 2007 President Musharraf declared an emergency rule across Pakistan and purported to suspend the Constitution, imposing martial law. In Islamabad, troops apparently entered the Supreme Court and were surrounding the judges' homes and opposition leaders like Benazir Bhutto, Imran Khan were put on house arrest. Justice Abdul Hameed Dogar has been appointed as the new chief justice of Pakistan, due to the refusal of the Iftikhar Muhammad Chaudhry to endorse the emergency order, declaring it unconstitutional, though he himself took oath under PCO in 1999.[31] In response, Pakistan was suspended from the councils of the Commonwealth of Nations on 22 November 2007.[32] In recent years, militant Islamists in the Tehreek-e-Nafaz-e-Shariat-e-Mohammadi (TNSM) organization, led by radical cleric Maulana Fazlullah have rebelled against the Pakistani government in Swat in the North-West Frontier Province. In 59 villages, the militants had set up a "parallel government" with Islamic courts imposing sharia law.

After a four-month truce ended in late September, 2007, fighting resumed.[33] The paramilitary Frontier Constabulary had been deployed to the area to quell the violence, but seemed ineffective. Militants were reported on November 16, 2007 to have captured Alpuri district headquarters in neighboring Shangla. The local police fled without resisting the advancing militant force which, in addition to local militants, also included Uzbek, Tajik and Chechen volunteers.[34] To roll back militantcy and restore order, the Government of Pakistan deployed a force from the regular Pakistani Army which was successful in retaking the lost territory, sending the Islamists into the mountains,[35][36] but attacks by suicide bombers on the Army continue.[37] It has been reported that the United States Special Operations Command is considering alternatives to render effective aid to Pakistan with respect to this and other Al Qaeda related insurgencies in the tribal areas of Pakistan, but prospects are uncertain.[38]