The most intriguing news with regard to special prosecutor Patrick Fitzgerald’s investigation of the apparent effort by the Bush-Cheney administration to punish former Ambassador Joe Wilson for revealing how the White House deceived the American people about the threat posed by Iraq is not the indictment of Vice President Dick Cheney’s chief of staff.

Make no mistake, it is exceptionally significant that Cheney’s closest aide and political confidante over the past two decades, I. Lewis “Scooter” Libby, has been charged with two counts of making false statements to federal agents, two counts of perjury and one count of obstruction of justice for misleading and deceiving the grand jury about how he learned that Wilson’s wife, Valerie Plame, was a Central Intelligence Agency operative.

Of course, it matters that Fitzgerald’s office says Libby lied “about how and when in 2003 he learned and subsequently disclosed to reporters then-classified information concerning the employment of Valerie (Plame) by the Central Intelligence Agency.” Of course it matters that, in response to these indictments, one of the most powerful players in Washington — the right-hand man of the vice president, a pioneering champion of the neo-conservative worldview and a principal architect of the war with Iraq — has resigned from his positions with the administration.

But what matters most are the questions that the Libby indictment has raised with regard to Cheney’s actions?

Let’s be clear: If the Libby indictment and resignation is all that comes of Fitzgerald’s two-year-long investigation into a case that touches on fundamental questions of government accountability, abuse of power and the dubious “case” that was made for going to war in Iraq, then this whole matter will be no more that a footnote to the sorry history of the Bush-Cheney era.

But Libby indictment is not necessarily all that will come of this investigation.

As Fitzgerald said during his press conference Friday, “It’s not over.”

Fitzgerald was extremely cautious about what he meant by that statement. But he did confirm that he will be keeping the “(grand)jury open to consider other matters.”

But, while Fitzgerald made the predictable announcement that that the “substantial work” of the investigation was done, the fact that the grand jury remains empaneled makes it reasonable to suggest, or at the very least to hope, that we have reached the Churchillian moment when it can be said: “This is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning.”

There will be those who are excited by the prospect that an extended investigation might actually “get” White House political czar Karl Rove, who has long been a subject of the inquiry but was spared indictment Friday. That’s very possible, as Fitzgerald has reportedly informed Rove’s lawyers that he is still under investigation.

But this will never be the inquiry that it can and should be if it merely tags Libby and Rove for wrongdoing.

The fundamental responsibility of the special prosecutor, and the one that he now has an opportunity to pursue, is to determine whether the Bush-Cheney administration set out to punish Wilson for exposing the fact that the president and the vice president had deliberately and dramatically inflated claims regarding Iraqi programs to develop weapons of mass destruction. Even David Gergen, the former adviser to presidents Nixon, Ford, Reagan and Clinton who is as cautious as the come in these matters, says that the indictments that have now been obtained in the case “raise questions about whether criminal acts were perpetrated to help get the country into war.”

The Congress and the media, which should have served as watchdogs on the administration before and after the start of the war, failed in their duty. And, while it is now commonly accepted that the president and the vice president stretched the truth to the breaking point in their feverish campaign to win support for action against Iraq, the specific details of the administration’s abuse of intelligence materials have yet to be adequately established. It is in the establishment of those details, and the facts surrounding them, that it becomes possible to understand why so many powerful people were so determined to destroy Wilson’s reputation and that of his wife. It is, as well, where questions about the precise roles of the president and the vice president in this whole sordid affair can, and must, be clarified.

Some details with regard to the vice president’s role have been revealed. The indictment indicates that Cheney was one of the first federal official who spoke with Libby about the identity of Joe Wilson’s wife. “On or about June 12, 2003, Libby was advised by the Vice President of the United States that Wilson’s wife worked at the Central Intelligence Agency in the Counterproliferation Division,” it explains. “Libby understood that the Vice President had learned this information from the CIA.”

The document goes on to point out that several of Libby’s most controversial calls to reporters appear to have taken place following conversations with Cheney. “On or about July 12, 2003,” the indictment says, “Libby flew with the Vice President and others to and from Norfolk, Virginia, on Air Force Two. On his return trip, Libby discussed with other officials aboard the plane what Libby should say in response to certain pending media inquiries, including questions from Time reporter Matthew Cooper.”

The indictment does not detail what was discussed in those conversations, and it does not get into who said exactly what. But it does note that Libby called both Cooper and Judith Miller of the New York Times, and that the Wilson’s wife was discussed during both those conversations.

Fitzgerald is careful to say, “We make no allegation that the vice president committed any criminal act.” But, as he explained, that is the “standard” response to questions regarding individuals who have not been indicted.

A review of the documents surrounding the Libby indictment leaves little doubt that there are still many questions to be answered, and that at least some of those questions should relate to the actions of the highest-ranking officials in the administration.

This is why 40 members of the U.S. House have urged Fitzgerald to expand the inquiry to examine whether Bush, Cheney and members of the White House’s Iraq War Group conspired to deceive Congress into authorizing the war – thus committing the federal crime of lying to Congress. Of course, there will be those who argue that such an investigation would be too broad an extension of the special prosecutor’s brief. But that’s just the latest line from those who have always wanted to close down this inquiry.

The simple fact is that, if Patrick Fitzgerald wants to get to the truth about who was behind the attempt to discredit Wilson and Plame, he has to examine the reason why the White House cared so very much about what was said regarding the use and misuse of intelligence. That is the examination that Fitzgerald can and should now begin.

John Nichols’ biography of Vice President Cheney, Dick: The Man Who Is President (The New Press, 2004) is currently available nationwide at independent bookstores and at www.amazon.com. An expanded paperback version of the book, which Publisher’s Weekly describes as “a Fahrenheit 9/11 for Cheney” and Esquire magazine says “reveals the inner Cheney,” will be available this fall under the title, The Rise and Rise of Richard B. Cheney: Unlocking the Mysteries of the Most Powerful Vice President in American History (The New Press).