To help appease India, which complained about US support for their neighboring foe, the US agreed to assist India, which is not a member of the nuclear non-proliferation treaty (NPT), in developing its nuclear program, thus further encouraging nuclear proliferation outside of the safeguards of the NPT and the International Atomic Energy Agency (IAEA).

In what was to become a major international scandal, it became known publicly that A.Q. Khan had organized a huge international nuclear black market, supplying materials and plans to countries such as North Korea, Iran, and Libya. Pakistan’s nuclear program was under the control of the military, and as many analysts observed, Musharraf’s denials that Khan’s ring had received official sanction strained credulity.

What became apparent was that Washington had struck yet another deal with Pakistan in which it would agree to Khan being made a scapegoat in exchange for Pakistan’s continuing ostensible support in the “war on terrorism”. Musharraf denied that the proliferation network had any official sanction and Khan echoed the official line and claimed all responsibility.  For his part, Khan was pardoned by Musharraf. Pakistan avoided heavy international criticism and sanctions for nuclear proliferation. And Washington was saved yet another major embarrassment.

Musharraf faced heavy criticism from overseas for not doing enough to combat terrorism and stem the growth of radical militancy, as well as heavy criticism at home for being complicit in the US’s war against Afghanistan, as well as for other perceived capitulations to the US such as backing away, at least rhetorically, from Pakistan’s Kashmir policy of supporting militants against India and its forces in the region. Musharraf was seen as engaging and arresting militants as necessary to appease Washington and to ease pressure from the US to do more to assist in the “war on terrorism” while at the same time allowing the very same militants to find safe haven.

A number of airstrikes by the US on Pakistani soil resulting in civilian deaths further enraged the local population against Musharraf and his alliance with Washington and helped to foster sympathy for the growing militant movement. Musharraf denied giving the US permission for the strikes to save face at home, but Washington insisted that the attacks were approved by Pakistan before execution.

In September 2006, Pakistan agreed to a truce with militants in North Waziristan, where the Taliban had declared the establishment of an “Islamic State” in February. Under the agreement, the militants were to end their cross-border activities and in return the government would not undertake any operations against them. The government also agreed to release prisoners and return confiscated weapons, vehicles, and other equipment to the militants.

Analysts predicted, since the accord had no enforcement measures and basically relied upon the militants’ word that they would cease in their activities against US and Afghan forces across the border while promising that their activities would not be monitored by the Pakistani government, that the result would be a consolidation of the extremists’ power in the region and an escalation of the threat of militancy and terrorism, which is precisely what occurred.

Musharraf calculated that he could appease the public, the militants, and his benefactors in Washington, but was only partially successful. The public became increasingly outraged about his perceived image as a puppet of Washington and increasingly weary of his dictatorial rule, longing for reforms leading to a more democratic government. The extremists perceived him as dishonoring their truce by taking actions designed to placate Washington (while of course ignoring their own obligations under the agreement). And while the White House publicly proclaimed its faith in Musharraf as a valuable ally, it was reported that through more private channels there was increasing pressure on him to deliver in order to justify the massive amounts of financial and military aid being sent to Pakistan each month.

In March 2007, Musharraf suspended the chief justice of the Supreme Court, Iftikhar Mohammed Chaudhry. Chaudhry was expected to oppose Musharraf’s plan to extend his presidency while remaining head of the army on the grounds that this would be unconstitutional. Chaudhry was also reportedly investigating the “disappearance” of many suspected militants, many of whom wound up under US custody at Baghram, Afghanistan or Guantanamo Bay, Cuba.

Musharraf’s decision was met with an enormous domestic outcry and the Supreme Court ruled in July that his suspension of Chaudhry was illegal and had him reinstated. The Supreme Court was then expected to challenge any attempt by Musharraf to be re-elected as President while keeping the title of army chief of staff.

Musharraf won reelection in an October Parliamentary vote, which was boycotted by his substantial opposition, many of whom walked out in protest since Musharraf was still in uniform. Most viewed the election as illegitimate and a minority of the Parliament representing Musharraf’s supporters actually participated in the election.

The Supreme Court was likewise expected to rule that the election was invalid since Musharraf had not resigned from his army role prior to the vote. Analysts predicted that Musharraf might declare a state of emergency in response to this threat to his authority, which is precisely what he did, citing the threat of extremism and terrorism as pretext.

In July 2007, the Pakistan military had raided the Red Mosque in Islamabad, where the ISI is based, and killed its radical cleric, Abdul Rashid Ghazi, after negotiations between the government and the cleric had broken down. The government had been a benefactor of the cleric and his mosque, but confronted Ghazi after militants had increasingly been terrorizing the local population with their strict interpretation of Sharia and carrying out abductions, including the kidnapping of several Chinese nationals the previous month.

 According to the government, hundreds of people were in the mosque, including women and children whom the militants were using as “human shields”. A spokesman said that more than a hundred men, women, and children came out of the mosque during the fighting. More than 100 people were also reported killed in the raid.

Al-Qaeda’s second-in-command Ayman al-Zawahri immediately condemned the raid in a videotape. Then in September, another videotape was released consisting of a montage of old video, including footage of bin Laden, who is heard in the beginning reciting verses from the Quran before another voice narrates what is purportedly a message from bin Laden likewise condemning Musharraf as a “traitor” and calling for his overthrow.

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