I don't know about the track record of Christopher Ketcham, the author of this Radar piece explaining the "big thing" that that made Jim Comey object to the warrantless wiretapping program so aggressively in March 2004. But it sounds like a plausible explanation.

Ketcham describes a database of Americans who, in case the government ever implements its Continuity of Government program in a time of national emergency, can be rounded up and jailed.

... a number of former government employees and intelligence sources with independent knowledge of domestic surveillance operations claim the program that caused the flap between Comey and the White House was related to a database of Americans who might be considered potential threats in the event of a national emergency. Sources familiar with the program say that the government's data gathering has been overzealous and probably conducted in violation of federal law and the protection from unreasonable search and seizure guaranteed by the Fourth Amendment.

According to a senior government official who served with high-level security clearances in five administrations, "There exists a database of Americans, who, often for the slightest and most trivial reason, are considered unfriendly, and who, in a time of panic, might be incarcerated. The database can identify and locate perceived 'enemies of the state' almost instantaneously." He and other sources tell Radar that the database is sometimes referred to by the code name Main Core. One knowledgeable source claims that 8 million Americans are now listed in Main Core as potentially suspect. In the event of a national emergency, these people could be subject to everything from heightened surveillance and tracking to direct questioning and possibly even detention.

[snip]

Another well-informed source—a former military operative regularly briefed by members of the intelligence community—says this particular program has roots going back at least to the 1980s and was set up with help from the Defense Intelligence Agency. He has been told that the program utilizes software that makes predictive judgments of targets' behavior and tracks their circle of associations with "social network analysis" and artificial intelligence modeling tools. [my emphasis]

Ketcham goes on to explain that the Bush Administration was cross-referencing Main Core with its warrantless wiretap program. I'm not entirely clear whether Ketcham is saying BushCo used Main Core to come up with potential targets of warrantless wiretapping, or whether they used the warrantless wiretapping intercepts to add to Main Core--I think, but am not positive--it's the latter.

A veteran CIA intelligence analyst who maintains active high-level clearances and serves as an advisor to the Department of Defense in the field of emerging technology tells Radar that during the 2004 hospital room drama, James Comey expressed concern over how this secret database was being used "to accumulate otherwise private data on non-targeted U.S. citizens for use at a future time." Though not specifically familiar with the name Main Core, he adds, "What was being requested of Comey for legal approval was exactly what a Main Core story would be." A source regularly briefed by people inside the intelligence community adds: "Comey had discovered that President Bush had authorized NSA to use a highly classified and compartmentalized Continuity of Government database on Americans in computerized searches of its domestic intercepts. [Comey] had concluded that the use of that 'Main Core' database compromised the legality of the overall NSA domestic surveillance project."

I agree with Digby: read the whole thing.

Now, like I said, I don't know how credible this story is, but two things seem to support its credibility.

First, the Continuity of Government thing is a big neocon wet dream. As Ketcham notes, Ollie North was an early operative developing the plan under Reagan. During their private sector years, Cheney and Rummy were both picked to run the government if the COG plan ever went into effect. So this would be, in a sense, Cheney's wet dream squared. He'd get to blow FISA away, as he and Addington apparently drool over doing. And he'd get to do so using his masters of the universe fantasy to boot. So it seems utterly plausible to me that Cheney would dream up merging all his wet dreams into one domestic spying program in the days after 9/11.

The other reason this seems so plausible is that, Ketcham quotes Philip Giraldi as speculating, it basically uses the Department of Homeland Security to shield this activity.

If Main Core does exist, says Philip Giraldi, a former CIA counterterrorism officer and an outspoken critic of the agency, the Department of Homeland Security (DHS) is its likely home. "If a master list is being compiled, it would have to be in a place where there are no legal issues"—the CIA and FBI would be restricted by oversight and accountability laws—"so I suspect it is at DHS, which as far as I know operates with no such restraints." Giraldi notes that DHS already maintains a central list of suspected terrorists and has been freely adding people who pose no reasonable threat to domestic security. "It's clear that DHS has the mandate for controlling and owning master lists. The process is not transparent, and the criteria for getting on the list are not clear."

This makes sense too. While anything run through a formal intelligence department would need to be--at least according to the laws Bush and Cheney like to ignore--reviewed by the Intelligence Committees. With DHS, those laws are more vague. Furthermore, this would put Michael Chertoff--who we know was brought into some of Yoo's crappy OLC opinions (albeit those that deal with torture), in charge of the program. In fact, Chertoff is basically implementing a different domestic spying program--that National Applications Office, which will use satellites within the US--over the objections of the House Homeland Security Committee (the Senate Homeland Security Committee--led by Joe Lieberman--seems to have no problems with Chertoff spying on us with satellites).

This explanation, in other words, fits neatly with a lot of things we know about the Bush Administration.