The complicated web entangling an ex-CIA director, a mistress, a military general and a woman he allegedly flirted with got no less confusing Wednesday, though the U.S. defense secretary insisted facts will emerge.

U.S. Secretary of Defense Leon Panetta defended his request to withhold Marine Gen. John Allen’s nomination to become NATO’s supreme allied commander, pending an investigation into Allen’s communications with a Florida woman.

The move was “a prudent measure until we can determine what the facts are, and we will,” Panetta told reporters Wednesday. “No one should leap to any conclusions.”

He added that the general “certainly has my continued confidence to lead our forces.”

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 CIA Director David Petraeus’ affair with a woman later identified as his biographer. Petraeus resigned Friday after acknowledging the affair.

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.

EXPLORING THE ALLEN AND KELLEY LINK

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 might involve 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 (Kelley) 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.”

Sources familiar with Kelley have said the relationship between the two was not sexual, but one said that the e-mails were flirtatious.

The fact that Allen remains 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.

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.

Both Allen and Petraeus appear to know Kelley’s sister, Natalie Khawam. The men wrote letters in support of the sister in a custody battle, court records show.

One of the sources familiar with Kelley said she first mentioned the alleged harassment in a casual conversation with an FBI agent she knew socially. She did not seek him out specifically for action on the matter, but he 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.

Kelley, 37, and her husband have released a statement saying they have been friends with Petraeus and his family for more than five years and asked for privacy.

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.

“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.”

PETRAEUS’ AFFAIR AND NATIONAL SECURITY QUESTIONS

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 home in Charlotte, North Carolina, late Monday, said local FBI spokeswoman Shelley Lynch. She declined to say what the agents were doing there.

A source told CNN national security contributor Fran Townsend that Broadwell was acting as Petraeus’ archivist, and that the FBI went to the house to look for any documents she might have. It was not clear whether any of the material was classified, the source said.

The Internet has been abuzz with video 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 disputed that notion.

“These detention claims are categorically not true. Nobody was ever held at the annex before, during, or after the attacks,” the official said.

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.

WHAT’S NEXT FOR PETRAEUS?

Petraeus was scheduled to testify on Capitol Hill this week about the Benghazi attack 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.

Senate Intelligence Committee Chairman Dianne Feinstein, D-California, said Tuesday that she hopes to bring Petraeus before the panel as early as Friday.