"Straight" didn't always mean flawless, of course. While "Cheney’s calm hand" on September 11th proved an asset, his advice on Iraq, nearly always in unanimity with Secretary of Defense Donald Rumsfeld, was obviously and demonstrably flawed. Cheney may not have run the show in the White House, but Bush clearly deferred on certain subject matters, like foreign affairs. The vice president tried to deflect any perception of his prominence to Baker.

Cheney said he never forgot that he was the vice president, and by all accounts he made a point of showing deference to Bush. While Bush called him “Dick,” Cheney always called Bush “Mr. President” and with others referred to him as “the Man.” (Karl Rove, though, reportedly referred to Cheney as “Management” — as in, “Better check with Management” — suggesting an influence not generally associated with vice presidents.)

Management and the Defense Department agreed on Iraq strategy. And when that strategy proved dangerous, Management's chief of staff, Scooter Libby, apparently tried to do a little damage control. In 2007, he was convicted of lying to investigators working to determine who'd leaked the identity of CIA agent Valerie Plame — a leak that served to undermine her husband's critiques of the war's progress.

By the time of Libby's conviction, the relationship between Cheney and Bush had fallen apart. After the 2006 midterms, in which Democratic candidates did unusually well in part as a rebuke from voters to the administration, Bush fired Rumsfeld. That firing happened without Cheney's input. Bush began seeking advice on international issues from Condoleezza Rice, "who supplanted Cheney as the president’s most influential lieutenant," Baker writes.

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.

Cheney, clearly an adherent to the principles of political loyalty, began to push Bush for a pardon of Libby shortly after his former aide's conviction. Bush commuted Libby's sentence, meaning that he'd never serve time in prison, but Cheney wanted more. As Bush's time in office ran out, and along with it his ability to grant that pardon, pressure from Cheney (and Libby) mounted. Bush deferred the decision as long as possible, twice rejecting the vice president's pleas directly and, more often, through surrogates. Eventually he gave Cheney his final answer in person. "You are leaving a good man wounded on the field of battle," Cheney responded to Bush, in what Baker calls perhaps "the harshest thing Cheney had ever said to him."

Certainly in part because of that conversation's proximity to Bush's last day in office — to which Baker says Bush responded, "Free at last" — the dispute was on Bush's mind as Obama was sworn in.

As the two men settled in and the vehicle began its slow, circuitous path past the barricades and out of the White House grounds, Bush took the opportunity to offer one last piece of advice. Whatever you do, Bush told Obama, make sure you set a pardon policy from the start and then stick to it. There Bush was, in the final minutes of his presidency, and foremost on his mind was the rift with his vice president.

Sometimes relationships don't work out as you might hope.

This article is from the archive of our partner The Wire.