Pakistani people gather at the site of suicide blast at Hub district some 16 miles from Karachi, July 19, 2007. At least 24 Pakistanis were killed when a suicide bomber hit a police-guarded convoy of Chinese workers in the country?s troubled southwest, police said. Photo: ASIF HASSAN/AFP/Getty Images

It is well known that Mr. Bush repeatedly praised Mr. 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 program and its deals with Al-Qaeda’s Pakistani tribal allies. Mr. Musharraf resigned from office Aug. 18 under the threat of impeachment.

The problem faced by the Bush administration when it came into office was that the Pakistani military, over which Mr. Musharraf presided, was the real terrorist nexus with the Taliban and Al-Qaeda. As Bruce Riedel, National Security Council senior director for South Asia in the Bill Clinton administration, who stayed on the National Security Council staff under the Bush administration, mentioned last September, Al-Qaeda “was a creation of the jihadist culture of the Pakistani army.”

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

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

After Sept. 11, the White House created the political myth that Mr. 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 Sept. 19, 2001, just six days after he had supposedly agreed to U.S. demands for cooperation against the Taliban regime and Al-Qaeda, Mr. 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, Mr. 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.

Mr. Musharraf also famously wrote that, immediately after Sept. 11, Undersecretary of State Richard Armitage had threatened to bomb Pakistan “back to the stone age” if Mr. Musharraf didn’t side with the United States against Osama bin Laden and his Afghan hosts. But Mr. 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, Mr. Musharraf played a complicated game. The CIA was allowed to operate in Pakistan’s border provinces to pursue Al-Qaeda operatives, but only so long as they had Inter-Services Intelligence units accompanying them. That restricted their ability to gather intelligence in the northwest frontier. At the same time, the Inter-Services Intelligence Directorate was allowing Taliban and Al-Qaeda leaders to operate freely in the tribal areas and even in Karachi.

The Bush administration also gave Mr. 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 Mr. Khan’s activities.

Journalists Douglas Frantz and Catherine Collins wrote in their book “The Nuclear Jihadist” that one retired general who had worked with Mr. Khan told them there was no question that Mr. 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 Mr. Musharraf cover up that inconvenient fact. According to CIA Director George Tenet’s memoirs, in September 2003, he confronted Mr. Musharraf with the evidence the CIA had gathered on Mr. Khan’s operation and made it clear he was expected to end its operations and arrest Mr. Khan.

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

That whole scenario had been “carefully orchestrated with Musharraf,” said Larry Wilkerson, then a State Department official but later Colin Powell’s chief of staff, in an interview last year. The deal that had been made did not require Mr. Musharraf to allow U.S. officials to interrogate Mr. 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 at a particularly advantageous moment for the administration. The New Republic magazine reported July 15, 2004, that a White House aide had told the visiting head of the Inter-Services Intelligence Directorate, Ehsan ul-Haq, that “it would be best if the arrest or killing of any (high value target) were announced on 26, 27 or 28 (of) July.” Those were the last three days of the Democratic National Convention.

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

Meanwhile, Mr. 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 President Bush chose to reward Mr. Musharraf by designating Pakistan as 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 organization 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 Mr. 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.