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When news of Pakistan’s clandestine program involving its top nuclear scientist selling rogue nations, such as Iran and North Korea, blueprints for building an atomic bomb was uncovered last month, the world’s leaders waited, with baited breath, to see what type of punishment President Bush would bestow upon Pakistan’s President Pervez Musharaf.

Bush has, after all, spent his entire term in office talking tough about countries and dictators that conceal weapons of mass destruction and even tougher on individuals who supply rogue nations and terrorists with the means to build WMDs. For all intents and purposes, Pakistan and Musharraf fit that description.

Remember, Bush accused Iraq of harboring a cache of WMDs, which was the primary reason the United States launched a preemptive strike there a year ago, and also claimed that Iraq may have given its WMDs to al-Qaeda terrorists and/or Syria, weapons that, Bush said, could be used to attack the U.S.

Bush, Vice President Dick Cheney and top members of the administration reacted with shock when they found out that Abdul Qadeer Khan, Pakistan’s top nuclear scientist, spent the past 15 years selling outlaw nations nuclear technology and equipment. So it was sort of a surprise when Bush, upon finding out about Khan’s proliferation of nuclear technology, let Pakistan off with a slap on the wrist. But it was all an act. In fact, it was actually a cover-up designed to shield Cheney because he knew about the proliferation for more than a decade and did nothing to stop it.

Like the terrorist attacks on 9-11, the Bush administration had mountains of evidence on Pakistan’s sales of nuclear technology and equipment to nations vilified by the U.S.—nations that are considered much more of a threat than Iraq—but turned a blind eye to the threat and allowed it to happen.

In 1989, the year Khan first started selling nuclear secrets on the black-market; Richard Barlow, a young intelligence analyst working for the Pentagon prepared a shocking report for Cheney, who was then working as Secretary of Defense under the first President Bush administration: Pakistan built an atomic bomb and was selling its nuclear equipment to countries the U.S. said was sponsoring terrorism.

But Barlow’s findings, as reported in a January 2002 story in the magazine Mother Jones, were “politically inconvenient.”

“A finding that Pakistan possessed a nuclear bomb would have triggered a congressionally mandated cutoff of aid to the country, a key ally in the CIA's efforts to support Afghan rebels fighting a pro-Soviet government. It also would have killed a $1.4-billion sale of F-16 fighter jets to Islamabad,” Mother Jones reported.

Ironically, Pakistan, critics say, was let off the hook last month so the U.S. could use its borders to hunt for al-Qaeda leader and 9-11 mastermind Osama bin Laden.

Cheney dismissed Barlow’s report because he desperately wanted to sell Pakistan the F-16 fighter planes. Several months later, a Pentagon official was told by Cheney to downplay Pakistan’s nuclear capabilities when he testified on the threat before Congress. Barlow complained to his bosses at the Pentagon and was fired.

“Three years later, in 1992, a high-ranking Pakistani official admitted that the country had developed the ability to assemble a nuclear weapon by 1987,” Mother Jones reported. “In 1998, Islamabad detonated its first bomb.”

During the time that Barlow prepared his report on Pakistan, Bryan Siebert an Energy Department analyst, was looking into Saddam Hussein's nuclear program in Iraq. Siebert concluded that "Iraq has a major effort under way to produce nuclear weapons," and said that the National Security Council should investigate his findings. But the Bush administration--which had been supporting Iraq as a counterweight to the Ayatollah Khomeini's Iran--ignored the report, the magazine reported.

"This was not a failure of intelligence," Barlow told Mother Jones. "The intelligence was in the system."

Cheney went to great lengths to cover-up Pakistan’s nuclear weaponry. In a New Yorker article published on March 29, 1993, investigative reporter Seymour Hersh quoted Barlow as saying that some high-ranking members inside the CIA and the Pentagon lied to Congress about Pakistan’s nuclear arsenal so as not to sacrifice the sale of the F-16 fighter planes to Islamabad, which was secretly equipped to deliver nuclear weapons. Pakistan’s nuclear capabilities and threat had become so grave by the spring of 1990 that then CIA deputy director Richard Kerr said the Pakistani nuclear threat was worse than the Cuban Missile crisis in the 1960s.

“It was the most dangerous nuclear situation we have ever faced since I’ve been in the U.S. government,” Kerr said in an interview with Hersh. “It may be as close as we’ve come to a nuclear exchange. It was far more frightening than the Cuban missile crisis.”

Presently, Kerr is leading the CIA’s review of prewar intelligence into the Iraqi threat cited by Bush.

Still, in l989 Cheney and others in the Pentagon and the CIA continued to hide the reality of Pakistan’s nuclear threat from members of Congress. Hersh explained in his lengthy New Yorker article that reasons behind the cover-up “revolves around the fact… that the Reagan Administration had dramatically aided Pakistan in its pursuit of the bomb.”

“President Reagan and his national-security aides saw the generals who ran Pakistan as loyal allies in the American proxy war against the Soviet Union in Afghanistan: driving the Russians out of Afghanistan was considered far more important than nagging Pakistan about its building of bombs. The Reagan Administration did more than forgo nagging, however; it looked the other way throughout the mid-nineteen-eighties as Pakistan assembled its nuclear arsenal with the aid of many millions of dollars’ worth of restricted, high-tech materials bought inside the United States. Such purchases have always been illegal, but Congress made breaking the law more costly in 1985, when it passed the Solarz Amendment to the Foreign Assistance Act (the amendment was proposed by former Representative Stephen J. Solarz, Democrat of New York), providing for the cutoff of all military and economic aid to purportedly non-nuclear nations that illegally export or attempt to export nuclear-related materials from the United States.”

“The government’s ability to keep the Pakistani nuclear-arms purchases in America secret is the more remarkable because (since 1989) the State Department, the Central Intelligence Agency, and the Defense Department (under Cheney) have been struggling with an internal account of illegal Pakistani procurement activities, given by a former C.I.A. intelligence officer named Richard M. Barlow,” Hersh reported. “Barlow… was dismayed to learn, at first hand, that State Department and agency officials were engaged in what he concluded was a pattern of lying to and misleading Congress about Pakistan’s nuclear-purchasing activities.”

Hersh interviewed scores of intelligence and administration officials for his March 1993 New Yorker story and many of those individuals confirmed Barlow’s claims that Pakistani nuclear purchases were deliberately withheld from Congress by Cheney and other officials, for fear of provoking a cutoff in military and economic aid that would adversely affect the prosecution of the war in Afghanistan.

It seems that today, Cheney is advising President Bush to deal with Pakistan’s nuclear proliferation much in the same way he did more than a decade ago. Give the country a pass, lie to the public about the seriousness of the matter and tell Pakistan you'll turn the other cheek if the country agrees to allow U.S. troops to use its borders to hunt for Bin Laden before the November election.

Jason Leopold spent two years covering California's electricity crisis and the Enron bankruptcy as bureau chief of Dow Jones Newswires.

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