Time Magazine reported yesterday that an inside mid-level source in al-Qaeda informed the US that the terrorist network built a device that would have turned New York's subway tunnels into a gas chamber that could have killed hundreds in an attack. Inexplicably, AQ's #2 Ayman al-Zawahiri called off the attack in 2003, but American analysts proved the design of the weapon could easily have worked:

It was time to call on Ali.

His handler contacted him through an elaborate set of signals, and a meeting was set up. cia operatives mentioned to him the names of the captives in Saudi Arabia and Bahrain, and the existence of the mubtakkar designs.

Ali said he might be able to help. He told his cia handlers that a Saudi radical had visited bin Laden's partner al-Zawahiri, in January 2003. The man ran the Arabian Peninsula for al-Qaeda, and one of his aliases was Swift Sword. Ali said the man's name was Yusef al-Ayeri. Finally, the United States had a name for Swift Sword.

This brought elation—a mystery solved, a case cracked—and then screams of pain. Al-Ayeri was in the Saudi group that had been released. They had had him. The Saudis let him go. But what Ali would next tell his American handlers would shape American policy and launch years of debate inside the White House. He said that al-Ayeri had come to tell al-Zawahiri of a plot that was well under way in the United States. It was a hydrogen cyanide attack planned for the New York City subways. The cell members had traveled to New York City through North Africa in the fall of 2002 and had thoroughly cased the locations for the attacks. The device would be the mubtakkar. There would be several placed in subway cars and other strategic locations and activated remotely. This was well past conception and early planning. The group was operational. They were 45 days from zero hour.

Then Ali told his handlers something that left intelligence officials speechless and vexed. Al-Zawahiri had called off the attacks. Ali did not know the precise explanation why. He just knew al-Zawahiri had called them off.

Ali then offered insights into the emerging structure of Islamic terrorist networks. The Saudi group in the United States was only loosely managed by al-Ayeri or al-Qaeda. They were part of a wider array of self-activated cells across Europe and the gulf, linked by an ideology of radicalism and violence, and by affection for bin Laden. They were affiliates, not tightly tied to a broader al-Qaeda structure, but still attentive to the wishes of bin Laden or al-Zawahiri. Al-Ayeri passed al-Zawahiri's message to the terror cell in the U.S. They backed off.

That was three years ago. When Bush demanded answers about the reasons why Zawahiri would have personally called off an attack of this magnitude on the subway system -- and why cells only loosely affiliated with AQ would have obeyed -- intel analysts could not come up with a single clear answer. The one option that made the most sense was that AQ had a much bigger attack in mind and did not want the subway attack to disrupt it with even tighter security response as AQ saw after 9/11. Bush asked them, "What could the bigger operation that Zawahiri didn't want to mess up?"

What, indeed? After three years, one has to assume that the larger operation either failed to coalesce or that AQ lost interest in staging it. Given the continual pressure the US has placed on al-Qaeda, the latter sounds rather silly, and even if true, the cells would have simply carried out the gas attack later. In 2005, New York announced greater security for the subway system in a move widely derided as a false alarm. Now, with this information, it looks like the intelligence community may have gotten information that the internal cell had reactivated the attack. It also would explain the terror alert just before the Republican National Convention in 2004, one that received some derision as an election-year ploy by the Bush administration.

I think we can now understand why the intel agencies felt so touchy during this period. Not only were they expecting a poison-gas attack, but they obviously worried about a much-larger attack of unknown character.

While the publication of this material may make us feel better about past terror alerts, one has to wonder about the release of the information about our humint within AQ. AJ Strata wonders if this has blown a valuable asset in the war on terror, a good question that will probably never get answered due to the nature of this conflict. I would think that the release of this information would indicate that this source has already gone cold, either killed or extracted by now. After all, three years in the organization as a double agent would be an intriguingly long run, and probably not realistic. The secondary effect of this release also might be beneficial; we may now have more humint sources within AQ, and now that AQ knows we penetrated their management once, they will likely have to start mole hunts to purge themselves of traitors -- a process that always leaves an organization damaged and less able to function, in the short run at a minimum. It could also be that 'Ali' was a composite of a number of sources.

AQ will have to guess at the truth, as we will -- and the results could devastate what's left of their structure.

Be sure to read the entire excerpt, published today. It will leave readers with a definite impression that our long run without an attack has been no accident, that our forces have done a good job (and been a little lucky) in their efforts to keep us safe. It also explains more why the NSA programs we use to discover these cells are highly valuable in giving us some means of discovering patterns of communications for the decentralized threats we face. With these enemies, we need to use all of the weapons we can muster to beat them before they can wrak their devastation on our homeland.

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