It’s been more than eight years since 9/11, but the fallout continues to reverberate throughout today’s New York. The Obama administration’s waffling over how to try Khalid Shaikh Mohammed, the attack’s mastermind, and the continuous, embarrassing delay in rebuilding the towers downtown have kept 9/11 more in the headlines than usual.

Now, as those political battles roll on, a new story about the run-up to 9/11 has emerged—a previously undisclosed, covert C.I.A. effort to recruit a spy to penetrate Al Qaeda a year and a half before the planes crashed into the towers.

The development is intriguing in part because the informant they were after was thought to be secretly gay—a fact that gave intelligence agents leverage in their efforts to turn him against his conservative Islamist circle. But the case may also help answer one of the long-standing mysteries of the 9/11 narrative: why a terrorist known to one part of the U.S. government wasn’t captured by other parts before he boarded a plane and helped carry out the most devastating attacks on the country.

Intelligence officials tell The Observer that the character at the center of the intrigue was an enigmatic but jovial man named Ahmad Hikmat Shakir, or “Shakir el Iraqi.” “He was tall as a mushroom, fat and gay,” one source familiar with the case told The Observer, “and the idea was to exploit him as an agent against Al Qaeda.”

The C.I.A.’s pursuit of Mr. Shakir, and the role he could have played in stopping, or at least complicating, the 9/11 plot, is a story that’s never been told, adding yet another piece in the puzzle leading up to the attacks.

Mr. Shakir’s story began on Jan. 5, 2000, at the Kuala Lumpur International Airport. He was there to meet a passenger on an incoming flight from Dubai—a Yemeni-born terrorist named Khalid al-Mihdhar. As it happens, the C.I.A. had its eyes on both of them.

Mr. Shakir didn’t have much, if any, of a file at the time. Few knew much about him, except that he was an Iraqi Arab, in his late 30s, with a dead-end job as a VIP greeter for Malaysian Airlines. But Mr. Mihdhar flashed big on the C.I.A.’s radar. At 25, he was already a deeply seasoned terrorist, with battlefield experience in Bosnia and time spent at various jihadi camps, and the agency knew that he’d come to Malaysia for some kind of special terror summit. The agency had one other key piece of intelligence: a U.S. visa had been stamped in Mr. Mihdhar’s green Saudi passport, meaning he almost certainly had been tapped for some kind of mission in America.

Indeed, it was this multiple-entry visa that would allow Mr. Mihdhar to come to America shortly after the C.I.A. started tracking him, and then, 18 months later, hijack an airliner as part of the 9/11 attacks.

Normally, the C.I.A. would have told the Federal Bureau of Investigation about the visa. That way he might have been arrested, or placed on a watch list, or at least questioned when he stepped into the U.S. Stopping him, some experts think, could well have stopped 9/11.

But the agency didn’t tell the F.B.I. about that visa, an act of omission that has baffled 9/11 buffs ever since.

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As the C.I.A. watched, Messrs. Mihdhar and Shakir climbed into a taxi outside the airport and drove to an upscale apartment complex near a golf course. For the next three days, Mr. Mihdhar and about half a dozen other high-level terrorists planned future strikes against America, including the hijackings of 9/11, according to multiple intelligence experts. In anti-terrorism circles, Kuala Lumpur is seen as a critical stop on the road to the attacks.

It’s uncertain whether Mr. Shakir participated in the meetings. But clearly, he was connected. And as the terror summit went on, the C.I.A. became convinced that it had found the perfect mole to help the agency crack the jihadi circle. Mr. Shakir seemed to have excellent contacts among the radical jihadists, and, according to intelligence sources, he certainly didn’t look like a terrorist or a spy.

Another source described Mr. Shakir to The Observer as a potential “access agent,” espionage jargon for an informant whose function is to spot other potential spies and turncoats. Though he may not know secrets or terrorist plots himself, the access agent is likely to know people who do, and is expected to facilitate meetings. As this officer explained, the agency “looked to him as a social broker.”

Mr. Shakir was no James Bond. In fact, he was short and fat and sociable, and was surmised to be gay, which would have opened him up to being flipped. (Mohamed Atta, the 9/11 hijacker from Egypt, was also rumored to be gay.)