FBI agents searched the Charlotte, N.C., house of David Petraeus’ ex-paramour Paula Broadwell Monday night, signaling a new twist in the extramarital affair that toppled the CIA boss.

Agents entered the house carrying boxes around 9 p.m. EST and were still there hours later, Reuters reported.

Federal officials had said in recent days that their investigation in the Petraeus affair was largely complete and that prosecutors deemed it unlikely they would bring charges in the case, which started as suspected cyber-harassment by Broadwell of Jill Kelley, a Petraeus friend.

Lawmakers and others have questioned whether Broadwell, who co-wrote a biography of the widely admired former general, obtained classified information from him or another source.

There was no sign that Broadwell or members of her family were at the house during the FBI search.

Shelley Lynch, a spokeswoman for the FBI in Charlotte, confirmed that agents were at the house but declined further comment, Reuters said.

Suspicions about Broadwell were raised on Oct. 26, when she publicly discussed previously unreported information about the Sept. 11 attack on the U.S. Consulate in Benghazi, Libya. In a speech at the University of Denver, she suggested the attack might actually have been an attempt to recover "Libyan militia members" who were being held by the CIA, the BBC reported.

"I don't know if a lot of you had heard this, but the CIA annex had actually taken a couple of Libyan militia members prisoner, and they think the attack on the consulate was an attempt to get these prisoners back," she said then. "It's still being vetted."

Her comments have stoked speculation as to whether there could be more to uncover about any role Petraeus had in the aftermath of the Benghazi attack.

The CIA denied the allegations, saying: "Any suggestion that the agency is still in the detention business is uninformed and baseless."

Meanwhile, the Wall Street Journal reported Monday night that the FBI agent who launched the investigation was excluded from the case over the summer due to his superiors' concerns that he was personally involved, according to officials familiar with the probe.

After being blocked from the case, the agent continued to press the matter, relaying his concerns to Rep. David Reichert, R-Wash., the officials said.

New details about how the Federal Bureau of Investigation handled the case suggest that even as the bureau delved into Petraeus' personal life, the agency had to address conduct by its own agent -- who allegedly sent shirtless photos of himself to Kelley prior to the investigation.

FBI officials declined to identify the agent, so he couldn't be reached to give his side of the story. The agent is now under investigation by the Office of Professional Responsibility, the internal-affairs arm of the FBI, two officials familiar with the matter told the Journal.

People close to Petraeus have said Kelley is a family friend and that there was no romantic relationship. It's unclear why Broadwell would have sent threatening emails to her, but she may have seen her as a rival for Petraeus' affections, the same people tell Reuters, speaking on condition of anonymity.

Kelley and her husband, Scott Kelley, a Tampa cancer surgeon, became friends with Petraeus and his wife, Holly, when he was stationed at MacDill Air Force Base in Tampa from 2008 until 2010, as commander of the Central Command, which runs operations in the Middle East and South Asia.

Unlike Broadwell, who has been silent and out of public view since the scandal broke Friday, Kelley has put out a statement on her family's friendship with the Petraeuses and asked that her family's privacy be respected.

A source close to the Kelleys told Reuters she is now being advised on how to respond to the uproar by one of Washington's top trial lawyers, Abbe Lowell, a family friend who has represented such powerful men as former Sen. John Edwards and disgraced Republican lobbyist Jack Abramoff. Lowell did not respond to requests for comment.

The confusion, shock and public humiliation caused by Petraeus’ affair may have hit no one as hard as his wife, Holly. By all accounts Mrs. Petraeus is devastated by the affair after almost four decades of marriage to her husband, who resigned as CIA director Friday afternoon.

“Well, as you can imagine, she’s not exactly pleased right now,” a family friend, retired U.S. Army Col. Steve Boylan said to ABC Monday morning. “In a conversation with David Petraeus this weekend, he said that, 'Furious would be an understatement.' And I think anyone that's been put in that situation would probably agree. He deeply hurt the family.”

Holly Petraeus met her eventual husband during a visit to West Point to visit her father, Gen. William Knowlton, who was superintendent of the school while Petraeus was studying there. Former classmate Conrad Crane told USA Today they met on a blind date.

“There was a superintendent with an attractive daughter and 4,000 lonely guys,” Crane said. “Dave was the one who got the girl.”

“I admired his intelligence and thought he was great. I had no way of predicting how far he would go,” Holly said in 2011. The two would go on to have two children together.

As her husband rose through the military ranks, Holly Petraeus lent her name to the cause of military families. Broadwell, during an appearance on the Don Imus radio show, even complemented Holly’s perseverance.

“He is married to Holly Petraeus, who is a wonderful military spouse and done so much for their children and for children of fallen soldiers, I respect her immensely,” Broadwell said while promoting her biography of the general, “All In.”

Holly testified in front of Congress when her husband was deployed in Iraq in 2003, according to the Daily Beast.

“My husband has been deployed 16 of the last 24 months,” she said. “This unrelenting pace of deployment is a retention issue. Families will not be willing to go it alone forever, with little relief in sight.”

Boylan said, according to the New York Daily News, he had spoken to Petraeus since the news broke Friday, and the general is “devastated” about what he’s done to his family and “knows he made a huge mistake.”