The Pakistani government's blanket denials became untenable as evidence mounted of illicit nuclear weapons technology transfers. It opened an investigation into Khan's activities, arguing that even if there had been wrongdoing, it had occurred without the Government of Pakistan's knowledge or approval. But critics noted that virtually all of Khan's overseas travels, to Iran, Libya, North Korea, Niger, Mali, and the Middle East, were on official Pakistan government aircraft which he commandeered at will, given the status he enjoyed in Pakistan. Often, he was accompanied by senior members of the Pakistan nuclear establishment.
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In early February 2004, the Government of Pakistan reported that Khan had signed a confession indicating that he had provided Iran, Libya, and North Korea with designs and technology to aid in nuclear weapons programs, and said that the government had not been complicit in the proliferation activities.
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On February 5, 2004, the day after Khan's televised confession, he was pardoned by Pakistani President Musharraf. However, Khan remained under house arrest.
The United States government imposed no sanctions on the Pakistani government following the confession and pardon. U.S. government officials said that in the War on Terrorism, it was not their goal to denounce or imprison people but "to get results." ... The U.S. also refrained from applying further direct pressure on Pakistan to disclose more about Khan's activities due to a strategic calculation that such pressure might topple President Musharraf.
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On July 4th, 2008 [after Musharraf's party lost the general election] he [Khan] in an interview blamed President Musharraf and Pakistan Army for the transfer of nuclear technology, he claimed that Musharraf was aware of all the deals and he was the "Big Boss" for those deals.