Now, the commander, Marine Gen. John Allen, is being investigated by the Defense Department, the woman who traded flirty e-mails with Allen is asking for privacy, and the home of the former spy chief's lover has been searched by the FBI.
Confused? You're not alone.
These are the latest developments in the complicated and widening scandal that began with CIA Director David Petraeus and two women with military connections, and has now ensnared Allen.
It also threatens to bog down a newly re-elected President Barack Obama. His administration is preparing for critical fiscal negotiations with Congress, but instead finds itself facing questions about sex scandals and dealing with powerful lawmakers increasingly concerned about potential security risks and why they weren't told of the Petraeus affair sooner.
"Well, I certainly wouldn't call it welcome," White House spokesman Jay Carney said in facing a blizzard of questions about Petraeus and Allen at Tuesday's press briefing.
The FBI informed defense officials about the allegations involving Allen on Sunday, the Defense Department said, and Defense Secretary Leon Panetta referred the issue to the department's inspector general for investigation.
According to the Defense Department, Allen is under investigation for what one defense official referred to as "flirtatious" e-mail messages with Jill Kelley, the woman whose complaints about anonymous, harassing e-mails led to the discovery of Petraeus' affair with a woman later identified as his biographer, Paula Broadwell.
Petraeus, a retired four-star general and Allen's former military boss at the U.S. Central Command, or CENTCOM, resigned Friday from his post at the CIA after acknowledging the affair.
Although Obama continues to have faith in Allen's leadership, he nevertheless put the Marine Corps general's nomination to become NATO's supreme allied commander on hold pending the outcome of the investigation, Carney said.
Allen will retain his post as the commander of U.S. and allied forces in Afghanistan, pending Senate confirmation of a successor, according to the Defense Department. That vote is due Thursday, Senate officials said.
Allen has denied wrongdoing, a senior defense official said.
The investigation into Allen is in its early stages, but 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 on Tuesday that many of the documents could be innocuous, involving routine business that Allen and Kelley were both involved in at the U.S. Central Command.
"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."
The potentially inappropriate messages were "flirtatious" in nature, a defense official who has been authorized to speak on the matter told CNN.
Sources familiar with Kelley have said the relationship between the two was not sexual. One said their communications were not of a sexual nature, while another allowed that the e-mails were flirtatious.
That Allen is remaining in command in Afghanistan suggests that there is no criminal issue, another U.S. official told CNN. But the official said the Defense Department's inspector general, an agency watchdog, could still find evidence of criminal conduct.
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.
"I think he ought to stay on unless there is some reason put forward that he has done something wrong, and then I think the military leaders will decide then what the actions will be," Carl Levin, D-Michigan, chairman of the Senate Armed Services Committee, said when asked whether he thought Allen should step down from his Afghanistan job.
Widespread media reports have described Kelley 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.
Kelley has not responded publicly to the latest news.
On Monday, her brother, David Khawam, told CNN affiliate KYW-TV that she went to authorities because she was scared after receiving the e-mails. He described his sister as a dedicated mother and said it would be "completely uncharacteristic" for her to have an affair.
One of the sources familiar with Kelley said she first mentioned the alleged harassment in a casual conversion with an FBI agent she knew socially. She did not seek him out specifically for action on the matter, but was happy for the help, the source said. The source added that Kelley did not know at first that the e-mails led to Petraeus.
Earlier, amid national talk about the Petraeus scandal, Kelley, 37, and her husband released a statement saying they have been friends with Petraeus and his family for more than five years and asked for privacy.
The sprawling story continued to sprout new details Tuesday, including a revelation from a senior official close to Allen claiming that it was Allen who received an anonymous e-mail about Kelley, and tipped her off that someone was threatening her.
Other U.S. officials have said Kelley received harassing e-mails that concerned her and went to the FBI.
"There is no affair," the senior official said. "She is a bored rich socialite involved with every single senior commander at CENTCOM, because she worked as an honorary ambassador."
Meanwhile, the FBI continues to look into the Petraeus affair amid congressional calls for an inquiry into why leaders were not notified of that matter sooner.
The Petraeus scandal also has raised questions about potential impacts on national security, including concerns that his paramour may have had access to his classified schedule and a New York Times report that she had classified documents on her laptop computer.
FBI agents were at Broadwell's Charlotte, North Carolina, home late Monday, said local FBI spokeswoman Shelley Lynch. She declined to say what the agents were doing there.
Also, a video has surfaced of a speech by Broadwell in which she suggested the Libya attack on September 11 was targeting a secret prison at the Benghazi consulate annex, raising unverified concerns about possible security leaks.
"I don't know if a lot of you have heard this, but the CIA annex had actually taken a couple of Libyan militia members prisoner and they think that the attack on the consulate was an effort to get these prisoners back," said Broadwell in a speech last month at the University of Denver.
A senior intelligence official told CNN on Monday, "These detention claims are categorically not true. Nobody was ever held at the annex before, during, or after the attacks."
Broadwell's source for that previously unpublished bit of information remains unclear, and there's no evidence so far that it came from Petraeus.
Administration officials have said the Benghazi assault was a terrorist attack.
Petraeus was scheduled to testify on Capitol Hill about the attack this week at closed-door hearings. 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.
Peter King, R-New York, said elements of the general's story "don't add up." King, who sits on the House Intelligence Committee, called Petraeus "an absolutely essential witness, maybe more than anybody else."
However, a senior U.S. official said Petraeus' departure wasn't connected to Benghazi hearings.
"Director Petraeus' frank and forthright letter of resignation stands on its own," said the official, who spoke on condition of anonymity because of the sensitivity of the topic. "Any suggestion that his departure has anything to do with criticism about Benghazi is completely baseless."
Senate Intelligence Committee Chairman Dianne Feinstein, D-California, said Tuesday that she hopes to bring Petraeus before the panel as early as Friday.
House Minority Leader Nancy Pelosi, D-California, added her voice to calls for an inquiry into the FBI investigation that unearthed the Petraeus affair, even though she does not believe formal reporting requirements were triggered.
"We have to find out what, who knew what when and why would Congress not have known," she said. "But again, again, if it doesn't involve national security, the notification requirement doesn't trigger. If it involves poor behavior, yeah, it would have been nice to know before we saw it on TV."
Section 501 of the National Security Act of 1947 spells out the requirements for the executive branch to inform the congressional intelligence committees of key intelligence-related activities.
"The president shall ensure that the congressional intelligence committees are kept fully and currently informed on the intelligence activities of the United States, including any significant anticipated intelligence activity as required by this title," the statute reads.
Panetta, who preceded Petraeus at the CIA, agreed with congressional calls for an inquiry.
"That's another issue I think we ought to look at, because as a former director of the CIA and having worked very closely with the intelligence committees, I believe that there is a responsibility to make sure that the intelligence committees are informed of issues that could affect ... the security of those intelligence operations," he told reporters while traveling in Australia.