Bush and Cheney were not friends.

Not since Richard Nixon and Henry Kissinger had two Americans in public office collaborated with such lasting effect as George Bush and Dick Cheney. In the aftermath of the Sept. 11 attacks, they confidently steered America through its most traumatic years since Vietnam, erecting a national-security apparatus that their successors have largely adopted and prosecuting wars in Afghanistan and Iraq that, members of the administration take pains to emphasize, toppled two brutal regimes. The continuing effects of their tenure are evident in some of the most vexing issues of today — what to do with the prisoners at Guantánamo Bay, how to balance the need for surveillance with the rights of private citizens and whether to use even a modest amount of force in Syria when the American public is tired of the costs of two long wars.

But if it was a partnership of enduring and controversial consequences, it was also one that was widely misunderstood. That their final hours together would be consumed by a private argument over the pardon of Scooter Libby underscores the distance the two men had traveled. Over the course of conducting hundreds of interviews with key players in the Bush White House, including Cheney, and examining thousands of pages of never-released notes, memos and other internal documents, I came to see a relationship that differs substantially from the commonly accepted narrative. Even in the early days, when a young, untested president relied on the advice of his seasoned No. 2, Cheney was hardly the puppeteer that critics imagined. To the extent that the vice president exerted outsize influence in the first term, he became more marginalized over the course of the second, as Bush sought new paths to right his troubled presidency.

Bush and Cheney were never quite friends. They did not see each other out of the workplace. Cheney did not spend social weekends at Camp David. On election night in 2000 and again in 2004, they watched the returns separately at first, coming together only late in the evening when they thought they could publicly claim victory. “They weren’t personally close,” said Ari Fleischer, the president’s first White House press secretary. “Cheney didn’t go jogging with George Bush. He was everything that Bush designed when he chose Dick Cheney to be counselor” — meaning a veteran Washington hand who would give him straight advice.

“It was professional, more than personal,” Cheney told me after leaving office, as he sat sipping coffee in a small library in his Virginia home. “We weren’t buddies in that sense.”