The FBI began a criminal investigation in February after discovering that Paula Broadwell, Petraeus' 40-year-old mistress and biographer, had accessed the former four-star general's email account. FBI officials also found harassing emails sent by Broadwell to another woman close to Petraeus. These emails, including one that referred to "sex under a desk," sparked the FBI investigation that ultimately ended the general's career in public service, RT said in a report.
But although the affair was uncovered months ago, Petraeus and government officials familiar with the matter kept quiet. The renowned intelligence director disclosed his relations with Broadwell and sent the president a letter of resignation on November 7 - the day after Obama was re-elected, and one week before he was scheduled to testify before Congress about what the CIA knew about the attack on the US Consulate in Benghazi, Libya that killed an ambassador and three staffers.
The director of national intelligence, James Clapper, had allegedly been told of the Petraeus investigation on election night and subsequently urged him to resign, senior intelligence officials told the Associated Press on condition of anonymity. US government officials claim that the White House and the CIA both remained uninformed of the FBI investigation until after the election.
An FBI insider told NBC News that Obama was in the dark about the affair until Wednesday.
"He made the decision to tell the White House. We handled it discretely," the official said, emphasizing that disclosing an affair that had not breached security was not the responsibility of the FBI.
But some believe the White House knew about the affair for much longer than they claim, and Congress is looking into the matter to determine if this is a major political cover-up delayed until after the election to protect Obama's presidency.
"The real question is, what did the president know, and when?" was the famous question from the Watergate scandal, which was repeated in the wake of Petraeus' resignation.
"It is hard to believe the White House did not know about this prior to the election," Frances Townsend, a former senior security official, told the Washington Times.
"What would he have told us? The resignation is incredibly convenient for the administration. Would he have revealed the CIA knew the Banghazi compound was under threat and Washington did nothing to secure it?" asked a senior Congressional staffer, as reported by the Daily Mail.
While questions over Obama's knowledge of the scandal linger, Senator Dianne Feinstein (D-Calif), head of the Senate Intelligence Committee, was distressed that she did not learn of the affair and planned resignation sooner. Petraeus had been scheduled to testify on the September 11 attack in Benghazi next week, and his resignation will have a significant impact on that hearing.
"It was like a lightning bolt," Feinstein said. She told Fox News Sunday that she wishes she had had time to plan for the CIA director's absence, and would have liked to have been briefed by the FBI sooner, the Associated Press reports.
Other members of the Congress have also expressed their frustration with the secrecy of the investigation, which they believe should have been exposed sooner.
"The FBI should have had an obligation to tell the president," House Homeland Security Chairman Rep Peter King (R-NY) told CNN. "It just doesn't add up."
Congress, by law, must be informed about "significant intelligence activities or failures." Lawmakers are wondering why the affair - which could have ties to a cyber crime and security breaches - was kept secret until the night of the election, and whether or not the White House knew about and supported the cover-up.
"There are strict rules, there is a wall, about sharing information on ongoing criminal investigations," an unnamed government official told the Wall Street Journal.
If some speculations are accurate and Petraeus resigned as a way out of testifying about the Libya attack - in an attempt to save the Obama administration from further criticism - then he still may not get off easy. Feinstein said she may still ask Petraeus to testify at a later date to get the much-needed information the now former director may have.
"I don't see how in the world you can find out what happened in Benghazi before, during and after the attack if General Petraeus doesn't testify," Graham told CBS.