It started in May with a spiteful email to the top US commander in Afghanistan. An anonymous writer warned Gen. John Allen that a friend with whom he was meeting in Washington the following week was trouble and he should stay away from her.

Allen thought the email was a joke because he didn’t know how anybody else would know about his personal plans with his friend, Florida socialite Jill Kelley, a person close to Kelley said.

That email started a chain of events that led to the downfall of CIA Director David Petraeus, put Allen’s career on hold and landed a decorated FBI agent in hot water for talking about an ongoing investigation.

The FBI traced that email and others of a similar vein to Paula Broadwell, Petraeus’ biographer, who agents would soon learn had also been his lover.

The fast-moving scandal broke just days after President Barack Obama was elected to a second term in office. Obama’s administration had been on the defensive for weeks because of a terror attack on the US Consulate in Benghazi, Libya, that left four Americans dead.

Briefings on the attack had been postponed until after the election and are now focused more immediately on Petraeus’ love life than on how terrorists were able to attack the poorly defended consulate.

Obama yesterday said he’s seen no evidence that national security was damaged by the revelations that ended his CIA director’s career and imperil that of his Afghanistan war commander.

But lawmakers aren’t taking Obama’s word for it and grilled FBI and CIA officials privately about the same issues: whether national security was jeopardised by the case and why they didn’t know about the investigation sooner.

The FBI’s investigation of the matter began last summer when Kelley turned over anonymous emails that had been sent to her and Allen.

The first anonymous email was sent to Allen in May, under the pseudonym “Kelleypatrol,” the person close to Kelley said, speaking on condition of anonymity because of the ongoing investigation.

In midsummer, Kelley shared these emails with an FBI agent, Frederick W. Humphries, whom she met at an FBI community programme in 2011.

Concerned that someone was tracking the movements of Allen and Petraeus, the FBI agent set the investigation in motion when he handed the information to the FBI’s cyber squad in Tampa. But Humphries was cut out of the loop and took that to mean the FBI was not taking the case seriously, the person close to Kelley said. Humphries would later reach out to Congress in a whistleblower role that has now landed him under internal scrutiny at the Bureau.

But the FBI was taking the case seriously and continues to investigate.

The FBI has found a substantial number of classified documents on Broadwell’s computer and in her home, according to a law enforcement official who spoke on condition of anonymity because the official was not authorised to speak publicly about the case.

Broadwell has told agents that she took classified documents out of security government buildings, the official said. Unauthorised possession of classified national defence documents is a crime. The Army has suspended Broadwell’s security clearance, which she had as a former Army intelligence officer.

The FBI also found emails between Kelley and Allen that were turned over to the Defence Department for investigation.

Obama has put on hold Allen’s nomination to become the next commander of US European Command as well as the NATO supreme allied commander in Europe until Pentagon investigators are able to sift through the emails that involve Allen and Kelley.

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