Gen. John Allen (left) and Gen. David Petraeus at Kabul International Airport, July 9, 2011 in Kabul, Afghanistan (Getty)
Journalist Paula Broadwell with Gen. David Petraeus. Petraeus resigned his post as CIA director on Nov. 9, 2012, admitting to an extramarital affair (Facebook/CBS News)
WASHINGTON (CBS News) -- CBS News has learned that during their affair, Gen. David Petraeus and his mistress Paula Broadwell used a cyber trick known to teenagers and terrorists in an effort to hide their communications.
Sources say they often composed draft emails which they both could read on a shared private email account -- without having to transmit the messages.
But, CBS News correspondent Bob Orr reports that six emails which Broadwell did send to Jill Kelley ultimately led FBI investigators to uncover the affair.
The scandal widened overnight. A Pentagon spokesman told reporters traveling with Defense Secretary Leon Panetta to Australia that America's top commander in Afghanistan was also being investigated for "potentially inappropriate" communications with Kelley.
"On Sunday, the Federal Bureau of Investigation referred to the Department of Defense a matter involving General John Allen, commander of the International Security Assistance Force (ISAF) in Afghanistan," Pentagon press secretary George Little told reporters.
The allegations against Allen are said to involve emails between him and Kelley written from 2010 to 2012. Asked if they were of a "sexual nature," a senior defense official would only say the messages were, "potentially inappropriate and they bare looking into. The Department is currently reviewing between 20,000 and 30,000 (pages of) documents connected to this matter."
CBS News senior correspondent John Miller, a former deputy director of national intelligence, says the investigation into Allen "is fallout" from the FBI's digging around in the inboxes of Petraeus and Broadwell.
He says the Pentagon realizes that if there is any indication of impropriety, they need it to come out now, not during Allen's confirmation hearing to become the next NATO commander - a nomination which has now been put on hold.
Allen has told Pentagon officials he has done nothing wrong, according to the official.
A married, four-star Marine general who took over from Petraeus as the top U.S. commander in Afghanistan in July 2011, Allen was in line to become NATO's Supreme Allied Commander for Europe. While that has been temporarily shelved, he will remain in charge of 68,000 U.S. troops in Afghanistan, pending the Pentagon's investigation.
Meanwhile, FBI officials searched Paula Broadwell's North Carolina home late Monday night. They left carrying several boxes.
Officials tell CBS News the scandal began to surface in June, when Broadwell emailed Kelley telling her to stay away from Petraeus. This was about the time Broadwell and Petraeus broke off their affair. Sources say that when Petraeus learned Broadwell was sending harassing emails to Kelley, he asked her to stop.
Kelley was spotted Monday leaving her Tampa home. She's not commented on the matter publicly but she has hired a high-powered legal team, including John Edwards' former counsel Abbe Lowell.
The man at the center of the scandal, Gen. Petraeus, has also remained silent. Friends and former aides who've spoken with him say the military commander did not intend to resign from the job until it was clear the scandal would go public. Now, they say he's extremely remorseful.
Col. Peter Mansoor worked directly with Petraeus from the summer of 2006 until 2008, and has spoken to him several times since the scandal came to light.
"He said, in those words, 'I screwed up. What I did was wrong. There's no excuses for it,'" Mansoor tells CBS News. "He's not gonna try to explain it away."
Mansoor says Broadwell was given unprecedented access to the top U.S. general.
"I thought it very odd that he would allow someone to have an extended embed with him... this thing morphed incrementally over time to where she was eventually almost considered a close member of the team," says Mansoor of the unconventional relationship.
And that was an impression Broadwell herself did little to try and contradict, even telling a crowd in Colorado, "a lot of my peers didn't know how to treat me, was I 'Major' Broadwell, or was I journalist Broadwell?"
Sources say Petraeus has stressed to friends that he only engaged in one affair, with Broadwell.
CBS News has also learned that one of the reasons the FBI was so concerned about Broadwell's emails to Jill Kelley, was that they contained private security information about Petraeus' travel schedule.
At first, agents thought someone must have broken into Petraeus' files, but it turns out Broadwell was likely just forwarding information the general had shared with her himself.