WASHINGTON, D.C.: The plot surrounding the resignation of Central Intelligence Agency (CIA) chief David Petraeus over an extramarital affair thickened on Sunday amid reports that his alleged lover had sent emails to a second woman she viewed as a threat to her love interest.

The affair came to light as the Federal Bureau of Investigation (FBI) was investigating whether a computer used by Petraeus—a married father of two—had been compromised, the New York Times and other US media reported, citing government officials.

US media reported that the FBI was focusing on Paula Broadwell, co-author of a favorable biography of Petraeus, for possible improper access to classified information.

Unnamed officials told the Times that Petraeus’s lover was Broadwell, a former Army major who spent long periods interviewing Petraeus for her book.

Broadwell, who is married herself and has two small children, offered no public comment on the revelations.

The Times and The Washington Post, citing an official briefed on the case, reported that the probe had been triggered by “harassing” emails sent by Broadwell to an unidentified second woman. The recipient of the emails was so frightened, The Post reported, that she went to the FBI for protection and to help track down the sender.

According to The Post, the second woman did not work at the CIA and her relationship with Petraeus remains unclear. However, the e-mails indicated that Broadwell perceived her as a threat to her relationship with the top spymaster, the paper said.

A senior intelligence official told the Times that US director of national intelligence James Clapper learned of the situation on Tuesday and had told Petraeus that “the right thing to do” would be to resign.

While Obama praised Petraeus as he acknowledged his departure, there was no denying it added to his headache over the makeup of his future administration, already expected to lose heavyweights such as Secretary of State Hillary Clinton.

Obama will likely have to replace not only Clinton, but also Defense Secretary Leon Panetta and Treasury Secretary Tim Geithner. Speculation is already rife about who will succeed Clinton, who has stressed she wants to reclaim a private life put on hold by decades in the spotlight.

Now, adding to the rumor mill is talk of who might follow in the footsteps of Petraeus, a 60-year-old former paratrooper credited with turning around the Iraq war.

His deputy Michael Morell will serve as acting CIA director, and is expected to fill in for Petraeus at an upcoming congressional hearing about the CIA’s alleged failure to protect a US consulate in Libya from a deadly September 11 attack that left four Americans dead, including Ambassador Chris Stevens.

One name being floated as a possible Petraeus replacement is John Brennan, the White House counter-terrorism adviser and a CIA veteran who has played an instrumental role in Obama’s drone war against al-Qaeda militants.