There is a hoary Texan aphorism that must now be striking resounding notes in George Bush's head. A new chief of staff, a change in the political mastermind Karl Rove's responsibilities, and a neophyte policy director are changes that can impress only the American President. If Bush were out in the Chihuahuan Desert of West Texas where he spent his childhood, he might hear someone in a coffee shop suggesting that "it's like puttin' earrings on a hog; there's some ugliness you just cain't hide".

And in Rove's case, it is likely to get uglier.

"Bush's Brain" has been operating as if he were out of danger in the federal investigation of the leaking of the name of Valerie Plame, an undercover CIA agent. (Plame's husband, Joe Wilson, had fallen out with the Bush regime, and the charge is that Bushites wanted to strike a blow at him by outing her.) But Rove is not out of trouble. In fact, the stoic prosecutor Patrick Fitzgerald may have evidence to make a case of perjury and obstruction of justice against Rove.

Fitzgerald's methodical, circumspect approach has made some people think that, after almost three years, he has decided not to indict. But he has had a lot on his plate. He has been in the midst of convicting an Illinois governor of corruption and is also investigating one of the country's largest media moguls. Rove has not been cleared; other cases were simply further along in the judicial process and demanded immediate attention.

If Rove was to be charged, it would be over an email he sent to Stephen Hadley, a former national security adviser. After an order from the White House counsel to turn over all relevant communications, and subpoenas from the federal grand jury, Rove still did not surrender this particular email. The apparent reason is that it shows the President's most trusted adviser to be considerably less than truthful with investigators. In all, Rove is believed to have given sworn testimony 10 times. In all but one of those instances, Rove said under oath that he did not speak to reporters about Valerie Plame until her name had been made public in a column written by his old friend, the conservative Robert Novak.

Unfortunately for Rove, the date on his email to Hadley offers at least one fact that contradicts his words and lays the foundation for likely criminal charges. The incriminating date gives the lie to the political strategist's claims that he did not talk about Valerie Plame until her name was already part of the national political discourse. In the 11 July 2003 communication, Rove confirms to Hadley that he spoke to Time magazine reporter Matthew Cooper three days before Robert Novak published his article outing Agent Plame. Cooper subsequently testified that he first learned of her identity from Rove.

Why did Rove not tell investigators about the email and the phone conversation with Cooper the first nine times he was placed under oath? His lawyer Robert Luskin has said Rove's memory was jogged much later by cocktail chatter, and prompted him and Rove to conduct "an exhaustive search" for evidence, which turned up the previously undisclosed email. No explanation was proffered as to why the note was not discovered under subpoena or why initial efforts were not equally "exhaustive". Rove said he simply forgot he had spoken to Cooper.

Nonsense.

A man who can remember precinct results from century-old presidential elections is not likely to forget he talked with one of Washington's most prominent journalists about a story that was a threat to the presidency. The more likely explanation is that Rove was playing a game he mastered early in his career, which is hiding behind a reporter's obligation to protect sources. But when Cooper agreed to speak to the grand jury, Rove's cover was blown. The strategist had no choice but to produce the email and an explanation as to why he had not mentioned it during previous testimony. And the best he could come up with was: "I forgot."

Last week Rove's supporters stopped assuring reporters that the legendary political magician was not going to be indicted. Fitzgerald's latest court paperwork also claims Rove will not be called as a prosecution witness in the Lewis "Scooter" Libby trial, a legal decision that strongly suggests an individual is headed for indictment. Further, the special prosecutor's documents intimate his inquiry might be looking at a conspiracy within the White House.

"Indeed, there exist documents," Fitzgerald wrote, "some of which have been provided to [Libby], and there were conversations in which the defendant participated that reveal a strong desire by many, including multiple people in the White House, to repudiate Mr Wilson before and after 14 July 2003."

Having reported on Rove for more than a quarter of a century, I am confident that no such activity could have transpired without his involvement and, more probably, his guidance.

As Rove's role was being redefined by the new White House chief of staff last week, Fitzgerald was reportedly presenting evidence against the political genius to the grand jury. Rove has been ordered by his new boss to concentrate his considerable political skills on the mid-term elections in November because the President's approval ratings are so poor that Republican candidates are running away from Mr Bush and his policies.

If, however, Fitzgerald's case against Rove is as open and shut as it appears from the outside, the man chosen to mastermind a comeback for the President and his party may find himself in legal jeopardy before the autumnal rhetoric of the election. And the President's final two years will accomplish little more than chopping down cedar trees on his Texas ranch.

Patrick Fitzgerald, too, carries an awful burden, even though he considers himself little more than a good citizen just doing his job. Untold millions of Americans are relying on this son of Irish immigrants to renew their faith that we remain a nation of laws. Too many of us have a well-earned cynicism; we see our country wandering desperately through a historical fog. We fear America has entered a permanent state of decline.

A little justice, though, might just begin a great renewal.

James C Moore is the co-author of 'Bush's Brain: How Karl Rove made George W Bush presidential'

Alan Watkins is away