In interviews and congressional appearances that followed, Johnson declined to directly talk about White House involvement. He said again and again, "The decision was mine and mine alone."

Critics didn't believe him.

Citing e-mails and testimony of others, some Senate Democrats said Johnson's testimony that he acted alone was suspicious - so suspicious they asked the FBI to investigate him for perjury, a case that remains open.

For Johnson, the California waiver decision marked the beginning of what would be a very rough year: The courts declared the pillars of his air pollution agenda illegal. The Union of Concerned Scientists issued a report documenting hundreds of instances of political interference with scientific work at EPA. When Johnson strengthened EPA ozone standards, his own scientists complained that he ignored their advice to make limits even stronger.

Exasperated, four Democratic senators, including Frank Lautenberg of New Jersey, called for Johnson's resignation.

"There are real human consequences whenever Administrator Johnson takes a dive," said Sen. Sheldon Whitehouse (D., R.I.)

On the Senate floor, he said: "We have seen EPA's clear mission darkened by the shadowy handiwork of the Bush White House - trampling on science, ignoring the facts, flouting the law, defying Congress and the courts while kneeling before industry polluters, and all for rank and venal purposes."

By late summer, congressional hearings took on such a prosecutorial tone that Johnson simply stopped showing up. At a final Senate oversight hearing in September, he refused to send anyone at all from the EPA.

"I wonder if he's still glad he took the job," mused Ruckelshaus.

Johnson said he is.

But he bristled at the specter of being the subject of an FBI investigation. When he was asked about it, his eyes narrowed. He said that hardball politics doesn't bother him, but that the personal attacks are unfair.

He isn't worried about the investigation, he said, because his testimony to Congress was accurate.

"I'm an experienced bureaucrat - very experienced bureaucrat - and I spend many hours practicing for hearings, and also have an outstanding command of the facts and figures," he said. "This too shall pass."

Johnson says this now - but eight months ago, he nearly resigned.

"Things were really wacky," said Gray, the assistant administrator for research. "It's a very difficult thing when people disagree with a science policy issue; they personalize it. Instead of being a disagreement about whether people are more like mice or rats, it's a question of: Is Steve Johnson a good person?"

Said Hazen, his longtime friend: "You can tell when someone is sagging under the weight of this."

Johnson said Bush told him to hang in there. The EPA administrator prayed about it, and one day, while riding to work in the SUV driven by his security detail, he found himself reading a book of inspirational quotes by Abraham Lincoln. Lincoln had said:

"I don't boast of being in God's will, I humbly pray that I am in his will."

Johnson took it as a sign that he should not resign.

"It was a providential reading," he said, "not an accident."