By the second term, though, as that vision came under fire with the deterioration of Iraq and the failure to find the weapons that led to the invasion, Bush moved away from Cheney and turned increasingly toward Secretary of State Condoleezza Rice, who supplanted Cheney as the president’s most influential lieutenant. No one in the White House had the relationship with Bush that Rice had. She worked out with him, talked sports with him, dined with him and Laura in the residence and spent weekends with them at Camp David. Over lunch one day in the first term, Rice told Christine Todd Whitman, then the Environmental Protection Agency administrator, “I can count on one hand the days when I have not spoken to the president over the last three years.” As Whitman later reflected: “She didn’t have a life. Her life was all about that.”

Bush turned to Rice to help repair the damage done by the administration’s aggressive response to the Sept. 11 attacks. “We had broken a lot of china,” Rice told me. “But at that point, you have to leave something in place. That is true with allies. It is true with the Middle East. It is true in putting together an international consensus on North Korea and international consensus on Iran. And I don’t think that is how the vice president saw it. I think he would have liked to have kept breaking china.”

Only by the end of his sixth year did Bush finally conclude that Rumsfeld had to go, a decision that represented the most fundamental break with Cheney, who was informed, not consulted. “It wasn’t open for discussion by the time he came to me,” Cheney told me. Cheney managed to preserve much of the national-security architecture he helped create, but he was now on defense more than offense, fending off changes that he thought would weaken the country or unravel the policies he had urged. “Perhaps my clout was diminished,” Cheney said in a 2011 television interview. “That’s possible. I wouldn’t quarrel about that.” Indeed, by the time they left office, Bush and Cheney disagreed on a long list of significant issues and policies. Where Bush was willing to pursue international diplomacy, empty secret C.I.A. prisons, sign an agreement to withdraw from Iraq and cut deals with Congress on military tribunals and warrantless eavesdropping, Cheney resisted any compromise as a sellout of the principles they once shared.

And then there was the Scooter Libby pardon.

A few weeks before Barack Obama’s inauguration, Joshua Bolten invited all of his predecessors to his office in the West Wing to meet with his successor, Rahm Emanuel. Thirteen of the living 16 men to have served as chief of staff attended, including Cheney, who was Gerald Ford’s top assistant. They went around the table one by one, offering advice. When Cheney’s turn came up, a devilish look crossed his face. “Whatever you do,” he said, “make sure you’ve got the vice president under control.”

As Bush’s final days in the White House approached, he did not exactly have his vice president under control. Cheney’s lobbying campaign on behalf of Scooter Libby had become deeply disconcerting to the president. To Cheney, it was a simple matter of justice. As he saw it, Libby had been pursued by an unprincipled prosecutor bent on damaging the White House. Neither Libby nor anyone else had been charged with the actual leak that precipitated the investigation, only with not testifying truthfully about how he learned about Wilson’s identity. Years later, it would be revealed that the special prosecutor, Patrick Fitzgerald, knew from nearly the start that Richard Armitage, Colin Powell’s deputy, was the original source of the leak, not Libby. Cheney believed that Fitzgerald’s relentless investigation in spite of this fact was proof that Cheney was the real target, and that Libby was caught in the cross-fire. Libby had loyally served his country, Cheney argued, only to be made into a criminal. And Powell and Armitage stayed quiet as it happened. “The Powell-Armitage thing was such a sense of betrayal,” Cheney’s daughter Liz told me. “They sat there and watched their colleagues in the White House — Scooter and everyone else — go through the ordeal of the investigation, and all that time they both knew Armitage was the leaker.” Armitage and Powell said they were simply following investigators’ instructions to keep silent.

As Cheney pressed Bush for the pardon, the president put him off by saying he would wait to issue controversial pardons until near the end of his term, which the vice president took as an indication that Libby would be among them. Bush had already commuted Libby’s prison sentence of two and a half years after it was handed down in 2007. As a result, Libby never had to spend a minute behind bars, a decision that inflamed critics on the left, who argued that Bush was interfering with justice, and on the right, who felt he had not gone far enough in quashing a bogus prosecution.

At the time, Bush said publicly that he was not substituting his judgment for that of the jury. So how would he explain a change of mind just 18 months later? That was the argument Ed Gillespie, the president’s counselor, made to Cheney when he came to explain why he was advising Bush against a pardon. “On top of that, the lawyers are not making the case for it,” Gillespie told Cheney, referring to the White House attorneys reviewing the case for Bush. “We’ll be asked, ‘Did the lawyers recommend it?’ And if the lawyers didn’t, it’s going to be hard to justify for the president.”