The scandal also has sparked an investigation into whether Marine Corps Gen. John Allen, the top U.S. commander in Afghanistan, sent inappropriate messages to a different woman, leading President Obama to put Allen's nomination to become NATO's supreme allied chief on hold.
The FBI uncovered the Petraeus affair while it investigated e-mails that his paramour, Paula Broadwell, allegedly sent to a Petraeus family friend, Jill Kelley, according to a U.S. official. Kelley, meanwhile, is the woman to whom Allen allegedly sent inappropriate e-mails, according to the Defense Department.
Below is a summary of what we know about the situation.
-- Despite his resignation as CIA director last week, Petraeus will testify Friday morning before the House Intelligence Committee and the Senate Intelligence Committee about the Benghazi attack.
-- A U.S. official told CNN that a CIA investigation of the "general conduct"of Petraeus includes whether he used agency resources in carrying out his affair with Broadwell.
-- The FBI is reviewing the actions of Frederick Humphries, the agent who triggered an investigation into e-mails received by Kelley, a law enforcement official said Thursday. The agency will look at whether Humphries followed proper procedures in speaking to some members of Congress about his concerns about how the agency was handling Kelley's case.
-- Petraeus says his resignation was not linked to the September attack that killed four Americans in Benghazi, Libya, HLN's Kyra Phillips reported Thursday.
The Petraeus affair
-- The FBI uncovered the affair between Petraeus, 60, and his biographer, Broadwell, 40, after Broadwell allegedly sent anonymous, harassing e-mails about Kelley -- first to Allen in May, and then to Kelley and her husband in June -- according to sources familiar with the case.
-- Allen told Kelley about the e-mail he received, and Kelley eventually told a FBI agent -- a friend of hers -- about the messages, sources say.
-- Kelley, 37, and her husband are friends of Petraeus and his family and friends of Allen. A Central Command spokesman said she is a volunteer with no official position at MacDill Air Force Base in Tampa, Florida, where the U.S. Central Command is headquartered.
-- The FBI determined that the messages came from Broadwell. One of the messages to Kelley was along the lines of "stay away from my guy," a U.S. official says.
-- During the investigation of the e-mails, other communications surfaced connecting Petraeus and Broadwell, a married mother of two living in North Carolina, an officer in the U.S. Army Reserve and a Ph.D. candidate in the Department of War Studies at King's College London.
-- Broadwell, a West Point graduate, had written a biography of Petraeus, published in January, called "All In: The Education of General David Petraeus." Having met Petraeus in 2006 when he spoke at Harvard, where she was a graduate student, she wrote the book after researching Petraeus for her Ph.D. dissertation on his leadership skills and visiting him and his team in Afghanistan, where he became top U.S. commander in 2010.
-- Petraeus and Broadwell began their affair in fall 2011, a few months after he returned to the United States, retired from the Army and took over at the CIA, according to a Petraeus friend. They ended it in summer 2012, Petraeus' friend said.
-- On Election Day, November 6, Petraeus told Director of National Intelligence James Clapper about the affair, according to a senior U.S. intelligence official. Clapper advised Petraeus to resign, the official said.
-- On November 9, Petraeus quit the CIA over the affair. The House and Senate intelligence committees were informed of the FBI investigation the same day.
-- Petraeus' resignation came just days before he was scheduled to testify before the Senate Intelligence Committee about the September 11 attack that killed four Americans at a U.S. diplomatic compound in Benghazi, Libya.
The Allen allegations
-- The Defense Department's inspector general is investigating allegations that Allen sent inappropriate messages to Kelley, the department said on Tuesday. The FBI told the department about the allegations on Sunday.
-- Allen has denied wrongdoing, a senior defense official said. Sources familiar with Kelley have said the relationship between the two was not sexual. Authorities are looking at the e-mails.
-- "There is no affair" between Allen and Kelley, a senior official close to Kelley said. "She is a bored rich socialite involved with every single senior commander at CentCom, because she worked as an honorary ambassador."
-- A U.S. official familiar with the e-mails Allen sent to Kelley said, "If they got out, John Allen would be very embarrassed by them." The official added that there was no evidence of physical contact between the two.
Investigations and fallout
-- Attorney General Eric Holder said Thursday that he didn't tell the White House about the Petraeus investigation because it was determined there was no threat to national security. "Had we made a determination that a threat to national security existed, we would of course had made that known to the president and to the appropriate members on the Hill," Holder told reporters.
-- Broadwell, an Army Reserve officer, has had her government security clearance suspended pending the outcome of ongoing investigations, two U.S. officials with direct knowledge told CNN's Barbara Starr on Wednesday.
-- Broadwell's affair with Petraeus has raised questions about whether it gave her access to national security information that she shouldn't have. The allegedly harassing e-mails detailed the "comings and goings of the generals and Ms. Kelley," according to a source. One of them was believed to be Petraeus, and because parts his schedule were not public, questions arose about whether the sender had access to sensitive information.
-- In a speech at the University of Denver at the end of October, Broadwell suggested the attack on the U.S. compound in Benghazi took place because the United States was housing Libyan prisoners there -- a theory, she noted, that had not been vetted yet. The claim has since been discounted by administration officials. Broadwell's source for that previously unpublished information remains unclear, and there's no evidence that it came from Petraeus.
-- Investigators have found classified information on a computer belonging to Broadwell, a law enforcement source told CNN national security contributor Fran Townsend on Wednesday.
-- A senior law enforcement official close to the Broadwell investigation said Wednesday night that materials taken from Broadwell's home were under review, and that it appeared unlikely she would be prosecuted for any unauthorized release of classified information.
-- On Tuesday, John Nagl, a retired military officer who worked for Petraeus for years and whom the former CIA director authorized to talk, said that Petraeus insists he never shared classified information with Broadwell.
-- Obama said Wednesday that he had seen no evidence of a potentially damaging breach in national security stemming from the affair involving Petraeus.
-- Obama also said Wednesday that Petraeus served his country with "great distinction," and he hoped that Petraeus' affair and resignation are "a single side note on what has otherwise been an extraordinary career."
-- Kelley's access to Florida's MacDill Air Force Base without an escort has been suspended, a Defense Department official said Wednesday. Kelley had been given special access to the base because of her position as a booster and promoter of programs to help U.S. troops, the official said.
-- Sen. Dianne Feinstein, D-California and chairwoman of the Senate Intelligence Committee, said she would investigate why the FBI did not notify congressional oversight committees about its investigation into Petraeus after the bureau determined he was having a secret extramarital affair.
-- Petraeus has not been following the media firestorm over the extramarital affair that led to his resignation. "He wants to maintain a distance and focus on his family at this time," his aide retired Col. Peter Mansoor said Wednesday.
-- While the nature of the relationship between Allen and Kelley, if any, is unclear, evidence of an affair could subject the general to military prosecution. Adultery is a violation of military law.
-- Obama has put Allen's nomination to become NATO's supreme allied commander on hold pending the outcome of the investigation, White House spokesman Jay Carney said on Tuesday.