by Gareth Porter

WASHINGTON - Pakistani President Pervez Musharraf's resignation Monday brings to an end an extraordinarily close relationship between Musharraf and the George W. Bush administration, in which Musharraf was lavished with political and economic benefits from the United States despite policies that were in sharp conflict with U.S. security interests. [1]

It is well known that Bush repeatedly praised Musharraf as the most loyal ally of the United States against terrorism, even though the Pakistani military was deeply compromised by its relationship with the Taliban and Pakistani Islamic militants.

What has not been reported is that the Bush administration covered up the Musharraf regime's involvement in the activities of the A. Q. Khan nuclear technology export programme and its deals with al Qaeda's Pakistani tribal allies.

The problem faced by the Bush administration when it came into office was that the Pakistani military, over which Musharraf presided, was the real terrorist nexus with the Taliban and al Qaeda. As Bruce Riedel, National Security Council (NSC) senior director for South Asia in the Bill Clinton administration, who stayed on the NSC staff under the Bush administration, observed in an interview with this writer last September, al Qaeda "was a creation of the jihadist culture of the Pakistani army".

If there was a state sponsor of al Qaeda, Riedel said, it was the Pakistani military, acting through its Inter-Services Intelligence (ISI) Directorate.

Vice President Dick Cheney and the neoconservative-dominated Bush Pentagon were aware of the intimate relationship between Musharraf's regime and both the Taliban and al Qaeda. But al Qaeda was not a high priority for the Bush administration.

After 9/11, the White House created the political myth that Musharraf, faced with a clear choice, had "joined the free world in fighting the terrorists". But as Asia expert Selig S. Harrison has pointed out, on Sep. 19, 2001, just six days after he had supposedly agreed to U.S. demands for cooperation against the Taliban regime and al Qaeda, Musharraf gave a televised speech in Urdu in which he declared, "We are trying our best to come out of this critical situation without any damage to Afghanistan and the Taliban."

In his memoirs, published in 2006, Musharraf revealed the seven specific demands he had been given and claimed that he had refused both "blanket overflight and landing rights" and the use of Pakistan's naval ports and air bases to conduct anti-terrorism operations.

Musharraf also famously wrote that, immediately after 9/11, Undersecretary of State Richard Armitage had threatened to bomb Pakistan "back to the stone age" if Musharraf didn't side with the United States against bin Laden and his Afghan hosts. But Armitage categorically denied to this writer, through his assistant, Kara Bue, that he had made any threat whatsoever, let alone a threat to retaliate militarily against Pakistan.

For the next few years, Musharraf played a complicated game. The CIA was allowed to operate in Pakistan's border provinces to pursue al Qaeda operatives, but only as long as they had ISI units accompanying them. That restricted their ability to gather intelligence in the northwest frontier. At the same time, ISI was allowing Taliban and al Qaeda leaders to operate freely in the tribal areas and even in Karachi.

The Bush administration also gave Musharraf and the military regime a free ride on the A. Q. Khan network's selling of nuclear technology to Libya and Iran, even though there was plenty of evidence that the generals had been fully aware of and supported Khan's activities.

Journalists Douglas Frantz and Catherine Collins wrote in their book "The Nuclear Jihadist" that one retired general who had worked with Khan told them there was no question that Khan had acted with the full knowledge of the military leadership. "Of course the military knew," the general said. "They helped him."

But the Bush administration chose to help Musharraf cover up that inconvenient fact. According to CIA Director George Tenet's memoirs, in September 2003, he confronted Musharraf with the evidence the CIA had gathered on Khan's operation and made it clear he was expected to end its operations and arrest Khan.

The following January and early February, Khan's house arrest, public confession of guilt and pardon by Musharraf was accompanied by an extraordinary series of statements by high-ranking Bush administration officials exonerating Musharraf and the military of any involvement in Khan's activities.

That whole scenario had been "carefully orchestrated with Musharraf", Larry Wilkerson, then a State Department official but later Colin Powell's chief of staff, told IPS in an interview last year. The deal that had been made did not require Musharraf to allow U.S. officials to interrogate Khan.

But the Bush administration apparently conveyed to the Pakistani military after that episode that it now expected the Musharraf regime to deliver high-ranking al Qaeda officials -- and to do so at a particularly advantageous moment for the administration. The New Republic magazine reported Jul. 15, 2004 that a White House aide had told the visiting head of ISI, Ehsan ul-Haq, that "it would be best if the arrest or killing of any HVT [high value target] were announced on 26, 27 or 28 July." Those were the last three days of the Democratic National Convention.

The military source added, "If we don't find these guys by the election, they are going to stick the whole nuclear mess up our a**hole."

Just hours before Democratic candidate John Kerry's acceptance speech, Pakistan announced the capture of an alleged al Qaeda leader.

Meanwhile, Musharraf was making a political pact with a five-party Islamic alliance in 2004 to ensure victory in state elections in the two border provinces where Islamic extremist influence was strongest. This explicit political accommodation, followed by a military withdrawal from South Waziristan, gave the pro-Taliban forces allied with al Qaeda in the region a free hand to recruit and train militants for war in Afghanistan.

Yet another deal with the Islamic extremists in 2006 strengthened the pro-Taliban forces even further.

But Bush chose to reward Musharraf by designating Pakistan a "Major Non-NATO Ally" in 2004 and by agreeing to sell the Pakistani Air Force 36 advanced F-16 fighter planes. Prior to that, Pakistan had been denied U.S. military technology for a decade.

In July 2007, a National Intelligence Estimate concluded that al Qaeda's new "safe haven" was in Pakistan's tribal areas and that the terrorist organisation had reconstituted its "homeland attack capability" there. That estimate ended the fiction that the Musharraf regime was firmly committed to combating al Qaeda in Pakistan.

Had the Bush administration accurately portrayed Musharraf's policies rather than hiding them, it would not have avoided the al Qaeda safe haven there. But it would have facilitated a more realistic debate about the real options available for U.S. policy.

Gareth Porter is an historian and national security policy analyst. His latest book, “Perils of Dominance: Imbalance of Power and the Road to War in Vietnam [2]“, was published in June 2005.

© 2008 Inter Press Service