Thus far it is undisputed that word of the Petraeus affair first reached the White House on Wednesday, Nov. 7, the day after Obama’s re-election, in a telephone call from Director of National Intelligence James Clapper Jr. to National Security Adviser Tom Donilon. Obama was celebrating with his family and staff in Chicago, and Donilon decided to hold the news until Thursday morning. Hours later, in the Oval Office, Obama told ­Petraeus he was not ready to accept the CIA chief’s resignation. “He wanted to sleep on it,” an Administration official says.

By Friday, there was no saving Petraeus. The Justice Department informed the White House Counsel’s office of the discovery of Allen’s voluminous correspondence with Kelley. Allen’s nomination for the NATO job, with Senate hearings set to begin within days, was put on hold and risked being withdrawn. It was the second time in three days that Obama had been caught unaware by long-simmering investigations within his government. “The President,” said White House spokesman Jay Carney, “was obviously surprised.”

Should Attorney General Holder have informed the President sooner? “I am withholding judgment,” the President told reporters. The unexpected discovery of Petraeus in the Kelley case put the Justice Department in a bind. Nobody wants to return to the days when J. Edgar Hoover used the secrets in his files for political advantage, so deciding what to tell the White House about the private lives of public figures requires great discretion. White House advisers say they are content for the Justice Department to follow its established protocols. But federal officials have offered conflicting and sometimes inaccurate explanations of what the protocols say.

One senior law-enforcement official says a 2007 memo by Bush Attorney General Michael Mukasey set strict limits on White House–Justice communication in criminal investigations. “Alerting the White House of an ongoing investigation? That’s a huge no-no,” the official says.

But the Mukasey memo said something quite different. In criminal cases, it said, Justice should balance the value of secrecy from the “law enforcement perspective” against the information “important for the performance of the President’s duties.” And in national-security cases, the memo specifically stated that no such restriction applied. Mukasey tells TIME that an ongoing extramarital affair by the CIA chief is a potential national-security issue. “They know enough at the point that his name turns up,” Mukasey says. “He’s doing it on a Gmail account, which any intelligence agency in the world would want to know about, and if they did know about, would feel in a position to use.”