Is James Comey really the civil liberties advocate he’s being made out to be?

With the White House’s decision to nominate James Comey as its next FBI director, the media has been stumbling over itself to recount a now-famous story in Washington about how Comey, while serving as the number-two official at the Justice Department, stood up to the Bush White House over the administration’s warrantless wiretapping program.

That story goes something like this. In March 2004, Bush administration officials were desperate to renew their warrantless wiretapping program, but some of their colleagues in the Justice Department refused to sign off on it. The White House decided to take the issue straight to Attorney General John Ashcroft, who was gravely ill in the hospital with gallstone pancreatitis. Comey, Ashcroft’s deputy, got wind of the plan and raced to the hospital to intercept the White House officials. The 6-foot-8 inch lawyer lumbered up the hospital stairs and beat White House Chief of Staff Andy Card and White House Counsel Alberto Gonzales to the room. Once there, Card and Gonzales did not acknowledge Comey. But Ashcroft refused to sign off on the order reauthorizing the program. Card and Gonzales left the room in silence.

The White House eventually went over Ashcroft’s head and pushed through the authorization anyway, prompting Comey and a group of other Justice Department officials to threaten to resign en masse if changes were not implemented to the program. It’s a confrontation that now stands out on Comey’s resume as a shining example of his commitment to civil liberties.

But is Comey really the fierce civil liberties advocate that his supporters will likely make him out to during his upcoming confirmation process? After all, it was Comey who oversaw the aggressive investigation into the leak of the covert CIA operative Valerie Plame’s identity — an investigation that ultimately resulted in the jailing of New York Times reporter Judith Miller. That piece of history should have civil rights advocates looking twice at Comey.

With White House political advisor Karl Rove at the center of an investigation into how columnist Robert Novak learned of Plame’s identity, Comey urged Ashcroft — who knew Rove back from when he had worked on Ashcroft’s senatorial campaign — to recuse himself from the case. Ashcroft heeded Comey’s advice, and Comey appointed his close friend (and the godfather to one of his children) Patrick Fitzgerald, a U.S. attorney in Chicago, to lead the investigation.

Fitzgerald carried out a meticulous and aggressive investigation that spared no one, including President George W. Bush and Vice President Dick Cheney, both of whom were interviewed as part of the probe. But that investigation also put Fitzgerald — and Comey — on a collision course with media freedoms. Refusing to reveal her sources to Fitzgerald, Miller was cited for contempt of court and spent 85 days in prison. And Miller wasn’t the only one — Time‘s Matthew Cooper very nearly landed in prison as well. Instead, he relented and revealed his sources at the last minute.

Comey is now in line to take over the FBI as the Justice Department is mired in a scandal over its decision to seize Associated Press phone records and to name a Fox News reporter as a co-conspirator, in cases that both center on unauthorized leaks of classified information. As in the Plame investigation, the government has shown a willingness to scale back First Amendment protections in pursuit of national security leaks — a tactic that Comey didn’t reject during his time in the Bush administration.

Crucially, Comey can claim some distance from Fitzgerald’s actions if the Plame case comes up during the confirmation process. While Fitzgerald provided Comey with periodic updates about the investigation’s progress, it appears Comey was not intimately involved in the probe and granted Fitzgerald a great deal of independence. That served the dual purpose of insulating the Justice Department from charges that it was trying to meddle with a politically explosive investigation while also distancing the agency from an investigation that was putting reporters in jail. Nonetheless, it is important to note that Comey had oversight powers of the investigation — Ashcroft had recused himself from the case — and that it was Comey who decided not to press charges against former State Department official Richard Armitage, the original source for the Novak column that outed Plame.

As the New York Times notes, Comey’s selection is politically expedient for the Obama administration. As a former Bush administration official, he is unlikely to elicit much opposition from Republicans in the Senate. And his record of standing up to the Bush White House is likely to endear him to Democrats.

But Comey’s last-minute stand against the wiretapping program isn’t the only episode from his career that might be aired before the Senate.