It was fall 2003. The news had broken that the Justice Department, at the request of the CIA, was investigating the leak that outed Valerie Wilson as an undercover intelligence officer, and FBI investigators were targeting White House officials. With a firestorm under way, I. Lewis “Scooter” Libby, Vice President Dick Cheney’s chief of staff, went to see his boss. Libby hadn’t passed any information about Valerie Wilson to right-wing columnist Robert Novak, who first published the leak in a July 14, 2003, column. But he had talked to other reporters about Valerie Wilson and her CIA connection before the leak occurred. And he also knew that Karl Rove, White House über-strategist, had spoken to Novak about her days before the leak column. That is, Libby knew a fair bit about the episode.

Libby told Cheney he had not been one of Novak’s two Administration sources for the leak, and he offered to disclose to the Vice President everything he knew. But Cheney did not want to hear it; Libby said no more.

Shortly after that, Libby, responding to a request from investigators, came across a note in his files indicating that in early June 2003–weeks before the Wilson affair began–Cheney had told him that the wife of former Ambassador Joseph Wilson worked at the CIA’s Counterproliferation Division, a unit of the agency’s clandestine operations directorate. (At that point, the former envoy had spoken only privately to two reporters about his CIA-sponsored trip to Niger, during which he had concluded there was not much to the intelligence report that Iraq had been uranium-shopping there.) The note was a significant discovery. A key issue in the investigation was who in the Bush Administration had spread information about Wilson’s wife to undermine Wilson’s charge that the White House had twisted the prewar intelligence (a criticism Wilson made public in a July 6, 2003, New York Times op-ed). And Libby had uncovered evidence showing that Cheney had conducted his own research on Joseph Wilson early on, learned about Valerie Wilson’s CIA job and shared the information with Libby. Cheney apparently was the first White House official to discuss Valerie Wilson’s specific place of work.

With a criminal investigation in full force, Libby told Cheney, I first heard about Valerie Wilson from you. From me? Cheney replied. The Vice President then tilted his head and, as Libby later said, “that was that.” The two discussed it no further.

These vignettes of how Cheney does business–in a mob-boss sort of way–emerged from the recently completed obstruction of justice trial of Scooter Libby. The former senior White House aide was found guilty of four of five counts in a criminal case narrowly focused on whether Libby had lied to the FBI and a grand jury when he claimed he had no official knowledge of Valerie Wilson’s CIA employment in the days before the leak and that he had merely shared with two reporters (Matt Cooper, then of Time, and Judith Miller, then of the New York Times) scuttlebutt about Wilson’s wife that he had heard from Meet the Press host Tim Russert.

The jury accepted the prosecution’s case that Libby had gathered information on Wilson’s wife before the leak and then–after a criminal investigation was launched–tried to conceal what he had done. But beyond resolving whether Libby had mounted a criminal cover-up to hide his–and perhaps Cheney’s–involvement in the leak episode, the trial exposed the inner world of Cheney’s crew. The proceedings also proved, beyond a reasonable doubt, that the Bush White House was neck-deep in the Valerie Wilson leak (even if Novak’s original source was then-Deputy Secretary of State Richard Armitage) and that the White House lied when it claimed otherwise.

Libby described his don’t ask, don’t tell meetings with Cheney during two appearances before the grand jury in 2004. For three days, jurors in the criminal trial listened to audiotapes of this testimony–and they could hear the disbelief in special prosecutor Patrick Fitzgerald’s voice as he questioned Libby about these conversations. After the leak investigation began, Fitzgerald noted, George W. Bush had requested that anyone with information come forward. So, the prosecutor asked, Why didn’t Cheney want to know what Libby knew? Libby had no explanation. Why didn’t Libby insist on spilling all to Cheney? The Vice President, Libby replied, had no desire for the information. Why didn’t Libby tell Cheney or anyone else in the White House that Rove had spoken to Novak about Valerie Wilson–especially since White House press secretary Scott McClellan had declared it “ridiculous” to suggest Rove had been involved in the leak? “It wasn’t what I was most concerned about,” Libby told the grand jury. The trial jurors listening to Libby on tape could have been forgiven for wondering if he and Cheney were adhering to an unspoken Sopranos-style version of plausible deniability.

Though Cheney was not on trial, his shadow draped the proceedings. Testimony and evidence showed that three months into the Iraq War–when no WMDs were being found and the situation in Iraq was deteriorating–the Vice President took it upon himself to counter Joseph Wilson’s criticism of the White House, even before Wilson went public. When Washington Post reporter Walter Pincus was sniffing around in early June 2003 to learn more about an unnamed ambassador who had gone to Niger because of a request from the Vice President, Cheney, after collecting information on his own about Wilson’s mission, dictated talking points to Libby. Libby then handed Pincus a semi-cover story: that it had been an aide to Cheney, not the Vice President, who had asked for more intelligence on the Niger charge a year before the war.

After Wilson’s op-ed created a stir, Cheney directed Libby to leak selective portions of the National Intelligence Estimate on Iraq’s WMDs to Judith Miller at a private breakfast meeting at the St. Regis Hotel on July 8, 2003. Cheney even went to Bush to have the President declassify the NIE for this private leak. This act of automatic executive declassification (known only to Bush, Cheney and Libby) was unprecedented, as Libby later told the grand jury. Rather than make the full NIE available to all the media, Cheney and Libby decided to share pieces that backed the Administration’s use of the Niger charge with a journalist who had reported stories supporting the Administration’s contention that Saddam’s Iraq was a storehouse of WMDs. They did not tell Miller that the NIE contained dissents on Niger and other WMD issues or that Cheney and Libby had recently received memos from the CIA indicating that the Niger intelligence had been spotty. It was at this meeting that Libby, according to Miller, told her for the second time that Wilson’s wife worked at the CIA.

Judith Miller ended up not writing about the NIE or Wilson’s wife. Her reporting had come under question within the Times. Selecting Miller for the handout, Libby told the grand jury, proved to be “a poor choice.” But Cheney was not done. As the war raged, he was busy managing his own damage control and wanted this material made public by a simpatico media outlet. So he ordered Libby to leak parts of the NIE to the editorial page of the Wall Street Journal. Libby, though, did not have a close relationship with the editors at the newspaper’s neoconnish editorial page. But Deputy Secretary of Defense Paul Wolfowitz did. At Libby’s direction, Wolfowitz disclosed slices of the NIE to the Journal. And the Journal dutifully ran an editorial that quoted from the not yet publicly available NIE to argue that Bush had been correct to cite the Niger charge in his prewar State of the Union address. “This information, by the way, does not come from the White House,” the editorial said. (Cheney and Libby were not sharing with their press contacts the information–also not yet public–that the CIA had repeatedly warned the White House not to include the Niger charge in earlier Bush speeches.)

During the Libby trial, a clear picture emerged: Cheney ran his own duchy within 1600 Pennsylvania Avenue. Libby had about a dozen national security aides working for the office of the Vice President–not the National Security Council. This was about double the staff that Vice President Al Gore maintained during the Clinton years. But more important, the OVP, as its denizens call it, independently pursued policies and developed press strategies. When the controversy exploded over Bush’s use of the Niger charge, Karl Rove and the White House senior staff pondered how to respond, but Cheney and Libby took their own steps, without always consulting Rove or National Security Adviser Condoleezza Rice. During his grand jury appearances, Libby described awkward (for him) meetings where senior White House aides discussed declassifying the NIE without realizing Cheney had already persuaded Bush to do this so Libby could slip it to selected outlets. (Cheney and Libby even cut Cathie Martin, Cheney’s communications director, out of the loop at key junctures.) Libby also told the grand jury he and Cheney might have discussed telling reporters about Valerie Wilson’s CIA employment–but that he could not recall having done so.

When the criminal investigation began in late September 2003, Cheney and Libby found themselves–at least momentarily–at odds with Bush’s senior aides. In the midst of the media frenzy, Scott McClellan declared publicly that Rove had not been involved in the leak. Libby, according to his grand jury testimony, wanted similar treatment–for, like Rove, he was the subject of media speculation about the leak’s origins. He went to McClellan and White House Chief of Staff Andrew Card and asked to be absolved publicly. They turned him down. Then Libby complained to his boss. Cheney wrote a brusque note–presumably for McClellan–that said, “Has to happen today. Call out to key press saying same thing about Scooter as Karl. Not going to protect one staffer & sacrifice the guy that was asked to stick his neck in the meat grinder because of the incompetence of others.” As Ted Wells, Libby’s lead lawyer, told the trial jurors, Cheney was angry that the White House was rallying around Rove but not Libby. In Cheney’s mind, Libby had leaked information to help the White House beat back the criticism that it had manipulated the case for war, and Cheney believed the CIA had screwed up by not yanking the Niger charge from the State of the Union speech. He didn’t want Libby twisting while Rove ducked.

But Cheney, looking to blame the CIA for the White House’s Niger problems, was in a bubble. He was ignoring the fact that the White House in mid-July 2003 had conceded that the CIA had repeatedly warned Bush’s speech writers and the National Security Council to excise the Niger allegation from Bush’s speeches before the State of the Union address. The Administration had surrendered, but Cheney and Libby were still fighting that war.

The White House did clear Libby within days, when McClellan said that he had spoken to both Rove and Libby “so that I could come back to you and say that they were not involved.” But this Cheney-facilitated declaration was not an accurate absolution. Nor was it any more honest than the White House claim, as enunciated by McClellan, that the leak was “not the way this White House operates” and that “if anyone in this Administration was involved in it, they would no longer be in this Administration.” The Libby trial presented evidence that at least three White House senior aides–Rove, Libby and Ari Fleischer, press secretary at the time of the leak–had spilled information about Valerie Wilson’s classified position at the CIA. This was indeed how the Bush White House operated–and Rove and Libby apparently did not tell McClellan the truth. “Rove lied,” Wells declared in his closing argument. Yet, as Wells noted early in the trial, Rove continued to work at the White House while his client ended up in the courtroom.

Before the trial started, at a December 19 court hearing, Wells declared, “We are calling the Vice President” as a witness. But this was more bravado than legal strategy. Cheney could have repeated on the witness stand his statement that Libby is “one of the most honest men I have ever met.” But how useful an endorsement would that have been coming from an unpopular politician who symbolizes the Administration’s credibility problems? Had Cheney taken the stand, Fitzgerald, during cross-examination, could have thrown a series of potentially embarrassing questions at him about his own part in the Wilson affair.

In fact, Fitzgerald had prepared for a cross-examination that would have lasted hours. But Cheney was spared by Team Libby–as was Rove. Though Wells suggested there had been a White House plot to get Libby (as well as a CIA plot, a State Department plot and an NBC News plot), he was not willing to put Cheney or Rove on the hot seat to prove the point (which apparently was beyond proving). In keeping Cheney and Rove out of the line of Fitzgerald’s fire, Wells managed to preserve Libby’s ultimate escape: a presidential pardon.

In his closing argument at the trial, Fitzgerald zeroed in on Cheney. Noting that Wells had accused the prosecution of placing a “cloud” over the Vice President, Fitzgerald declared, “There is a cloud over what the Vice President did.” Cheney’s and Libby’s actions had caused Fitzgerald to be suspicious of Cheney’s involvement in the leak episode. “We didn’t put that cloud there,” Fitzgerald told the jury. “That cloud remains because the defendant has obstructed justice and lied about what happened.” It seemed that Fitzgerald believed he had not been able to sort out fully Cheney’s participation because Libby misled the investigators. Libby was no fall guy for Rove, Fitzgerald was saying; he covered up for Cheney. And this “cloud,” Fitzgerald noted, continued to rest above the White House. “Don’t you think,” Fitzgerald asked the jurors, “the FBI, the grand jury, the American people are entitled to a straight answer” about who did what in the leak episode?

The straight answer never came. After Valerie Wilson’s cover was blown, outraged Congressional Democrats demanded a special prosecutor be appointed to investigate and uncover what had transpired–but they miscalculated. Fitzgerald’s job was not to ascertain the full truth but to determine if a crime had been committed and if anyone ought to be prosecuted. That mission drove him to subpoena journalists and even imprison Judith Miller for eighty-five days–establishing what could be a troubling precedent for other prosecutors and reporters. But from his perspective, he had little choice. Fitzgerald believed Cheney’s top aide had lied to the FBI and a grand jury to protect himself and possibly the Vice President (and Fitzgerald suspected Rove had also misled the investigators). Fitzgerald felt he couldn’t walk away from this perjury, even if he could not indict anyone for the actual leak, and he concluded that he needed the testimony of several reporters to determine if Cheney’s chief of staff had tried to stonewall a criminal investigation related to a national security matter.

Still, Fitzgerald’s investigation and the subsequent trial were not designed to provide the public with the complete story. The public, for example, has not learned how Rove managed to keep his job; what Bush did or did not know about Rove’s part in the leak; or what Bush and Cheney told Fitzgerald when he questioned them.

At the end of his closing argument, Wells got weepy. After declaring Libby to be the victim of a run-amok prosecutor who had relied on witnesses with faulty memories, he asked the jurors, “Give him back to me. Just give him back.” He choked back a sob. Responding to Wells’s melodrama, Fitzgerald argued to the jury that Libby “stole the truth from the judicial system…. Your verdict can give truth back.”

After ten days of deliberation, the jurors gave Fitzgerald what he desired. Though the case–as lawyers on both sides repeatedly stated–was not about the Iraq War and the White House’s credibility, it was about the truthfulness of Cheney’s senior aide, whose lies emerged from the Administration’s effort to defend itself from the charge it had misled the nation into war. The verdict that now hangs over Scooter Libby is also a cloud that darkens the sky above the President and the Vice President.