The extra-marital affair that prompted the shocking resignation of CIA Director David Petraeus was carried on with a journalist who was covering him and became the subject of an FBI investigation dating to Spring 2011.
This according Newsmax Washington correspondent Ronald Kessler, who cites his FBI source:
...the investigation began when American intelligence mistook an email Petraeus had sent to his girlfriend as a reference to corruption. Petraeus was commander of U.S. Forces in Afghanistan from July 4, 2010 until July 18, 2011. The investigation began last spring, but the FBI then pored over his emails when he was stationed in Afghanistan. The woman who was having an affair with Petraeus is a journalist who had been writing about him.
The FBI was concerned for national security but also turned up some steamy dirt, including an email reference to "sex under a desk."