The FBI opened the investigation after learning the Mistress was emailing government official. The investigation concluded when they determined no laws had been violated, no one was being stalked or coerced.
Investigation over, case closed, then just before testimony, at least a year after the affair began Petraus resigns abruptly, after an admiral allegedly involved was re-assigned.
Petraus said the reason was "strictly personal" no connection, but what would he say? Maybe he didn't fancy Fort Marcy Park in the Winter for a "suicide" about his personal guilt?