Retired Army Gen. David Petraeus resigned from his CIA director post last week after an FBI investigation revealed he had an extramarital affair, an investigation that also prompted questions about whether his paramour had inappropriate access to classified information.

The scandal also has prompted an investigation into whether Marine Corps Gen. John Allen, the top U.S. commander in Afghanistan, sent inappropriate messages to a different woman, prompting 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 Petraeus affair, the Allen allegations, and the investigations and fallout.

The Petraeus affair

-- The FBI uncovered an affair between Petraeus, 60, and Petraeus biographer Paula Broadwell, 40, after Broadwell allegedly sent anonymous, harassing e-mails to Kelley in May, a U.S. official says. A senior official close to Allen says it was Allen who received an anonymous e-mail about Kelley, and tipped Kelley off that someone was threatening her.

-- Kelley, 37, says she and her husband have been friends of Petraeus and his family for five years. Widepsread media reports have described her as a liaison at MacDill Air Force Base in Tampa, Florida, where the U.S. Central Command is headquartered. Both Petraeus and Allen were previously stationed at the base. A Central Command spokesman said she is a volunteer with no official position.

-- Investigators eventually traced the e-mails to Broadwell, a U.S. official said. The messages were along the lines of "stay away from my guy," but not explicitly threatening, according to a U.S. official.

-- During the investigation, other communications surfaced between 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." She wrote the book after researching, visiting and interviewing Petraeus for her Ph.D. dissertation on his leadership skills.

-- Broadwell met then-Gen. Petraeus in Spring 2006 when he spoke at Harvard, where she was a graduate student, according to the preface of her book. She told the general about her research interests.

-- In 2008, she began her dissertation on him, interviewing him by e-mail and during occasional jogs with him, including one they took with his team along the Potomac River in Washington.

-- In 2010, Petraeus hwas tapped to replace Gen. Stanley McChrystal as the top commander in Afghanistan. Broadwell decided to turn her research into a book and follow Petraeus to that country. She spent months in Afghanistan interviewing Petraeus and others for her book, which she wrote with Vernon Loeb.

-- In August 2011, Petraeus retired from the U.S. Army and left Afghanistan. The next month, Petraeus was sworn in as CIA director and returned to the Washington area.

-- Petraeus and Broadwell began their affair in fall 2011, about two months after he took over at the CIA, according to a Petraeus friend.

-- Broadwell and Petraeus ended their affair in summer 2012, a decision reached mutually, and the two last talked about a month ago, Petraeus' friend said.

-- FBI investigators, following up on the anonymous e-mails to Kelley, interviewed Broadwell twice this fall, a U.S. official said. They also gained access to her computer and discovered e-mails that turned out to be from Petraeus, who also was interviewed once, a U.S. official said. A source told CNN national security contributor Fran Townsend that Paula Broadwell was acting as Petraeus' archivist, and that the FBI went to Broadwell's house November 12 to look for any documents she might have. It was not clear whether any of the material there was classified, the source 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 then advised Petraeus to resign, the official said.

-- On November 9, Petraeus quit the CIA, admitting to an affair. The House and Senate intelligence committees were informed of the FBI investigation the same day, prompting outrage from House and Senate members.

-- 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 Gen. John Allen, the top U.S. commander in Afghanistan, sent inappropriate messages to Kelley, the department said November 13. The FBI told the department about the allegations on November 11.

-- The potentially inappropriate messages were "flirtatious" in nature, a defense official who has been authorized to speak on the matter told CNN.

-- Allen has denied wrongdoing, a senior defense official said.

-- Authorities are looking into some 20,000 to 30,000 pages of documents, a defense official told CNN. It is not clear how many of those include potentially inappropriate communications.

-- A U.S. official told CNN that many of the documents could be innocuous, involving routine business that Allen and Kelley were both involved in at U.S. Central Command, or CENTCOM. "In his duties at CENTCOM, Gen. Allen conducted a lot of legitimate business. She did a lot of work with CENTCOM, including Wounded Warriors and such," the official said. "It could be that 29,900 of the documents are legitimate business, and the few remaining raise a few eyebrows."

-- "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."

-- Kelley's brother, David Khawam, told CNN affiliate KYW-TV on November 12 that she is a dedicated mother and said it would be "completely uncharacteristic" for her to have an affair. He said that she reported the other e-mails -- the anonymous ones that the FBI allegedly linked to Broadwell -- because she was scared.

Investigations and fallout

-- Broadwell's affair with Petraeus has raised questions about whether the affair gave her access to national security information that she shouldn't have. The allegedly harassing e-mails that the FBI allegedly tracked to Broadwell detailed the "comings and goings of the generals and Ms. Kelley," according to a source with knowledge of the messages. Among those believed to be referenced in the e-mails was Petraeus. Because parts of Petreaus' schedule were not public, the e-mails raised questions about whether the sender of the e-mails had access to his private schedule or other 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 at the time, that had not been vetted yet. The claim by Broadwell has since been discounted by administration officials. Broadwell's source for that previously unpublished information remains unclear, and there's no evidence so far that it came from Petraeus.

-- A senior U.S. intelligence official said Broadwell did not have a security clearance from the CIA. Another official said Broadwell, who is an officer in the Army Reserve, did have some kind of security clearance and that there are no issues with Broadwell having unauthorized access to classified information.

-- "I do not know how she got that information," said Sen. Dianne Feinstein, D-California and chair of the Senate Intelligence Committee, referring to Broadwell's October speech. "We should find out."

-- Feinstein 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.

-- According to a congressional aide familiar with the matter, the House and Senate intelligence committees weren't informed that there was an FBI investigation into the situation until the day Petraeus resigned.

-- Petraeus was scheduled to testify before Congress on the Benghazi attack and the government's response to it, but because he resigned as CIA director, he won't testify as scheduled. Some Republicans have criticized the administration's response to the Benghazi attack and have speculated that the timing of Petraeus' departure was linked to the congressional inquiry. Rep. Peter King, R-New York, said elements of the general's story "don't add up." He called Petraeus "an absolutely essential witness, maybe more than anybody else."

-- Feinstein said that she still hopes to bring Petraeus to testify about the Benghazi attack on November 16.

-- 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.

-- President Barack 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 November 13.

-- Allen will retain his post as the commander of U.S. and allied forces in Afghanistan pending Senate confirmation of a successor, who was nominated in October, before news of the allegations broke, according to the Defense Department. That vote is due November 15, Senate officials said.