I’ve run across a lot of confusion about the Patraeus affair situation, revolving around the question of “why did he resign over an affair; is that really a big deal anymore?”

Well, off the top of my head, I can think of five reasonable explanations why he might have resigned over this scandal, none of which have anything to do with an “attempted cover up”:

1) Perjury.  People who have high level security clearances are vulnerable to blackmail by those who might want access to the information that they possess.  This is one of the big reasons that the government does thorough background checks before anyone can get a security clearance–to make sure that there are no skeletons in that person’s closet.  The government doesn’t really care if you are gay, or if you smoked pot in college, or if you had an affair.  But they do care if you’re hiding the fact that you’re gay, or if you don’t want people to know that you smoked pot in college, or if you haven’t come clean about your affair to your family–because those kind of secrets create blackmail opportunities.  Lying on a security clearance application is considered perjury, and is a crime.  So, if General Patraeus hid his affair from those doing the background check on him (and the better your clearance, the more often and the more thorough the background checks–so he would have certainly had one since the affair began), then yes, that is reason enough to be fired.

2) “Pillow Talk.”  In the course of the investigation, the FBI has found that Ms. Broadwell, the woman he had the affair with, was in possession of a lot of classified information that she shouldn’t have had access to.  The FBI has said that they have no intention (so far) of charging Patraeus with a crime–but to say “they won’t be charging him” is different than saying “he didn’t tell her anything.”  If Patraeus shared classified information with his mistress, even if prosecutors decide not to charge him with anything, then it is very reasonable that he should resign his post as head of the CIA.

3) The Military Code of Justice.  Having an affair is not against the law.  But it is a violation of the Military Code of Justice, which governs behavior for all those in the military.  General Patraeus is now retired from the military–but he was still active when the affair began.  I have no reason to believe that the military would charge him with anything post-retirement–but as someone who reportedly took his honor very seriously, I could easily imagine a man like General Patraeus deciding that because he violated the rules, and that some punishment was in order.  In other words, resigning could have been an act of self-flagellation.

4) Retirement.  Many top cabinet officials have stepped down anyway (The Secretaries of State, Defense, and Treasury, among others); it is common for cabinet officials to take the reelection as an opportunity to go do something else for awhile.  It is very possible that Patraeus was planning on retiring anyway–and that the affair and the scandal just sped up the timeline of something he wanted to do anyway.  After all, if the Obama Administration had started putting political capital into his defense, they would have been upset at him for resigning in the middle of the scandal.  Better to resign now.

5) Personal Affairs.  Patraeus is still married.  Director of the CIA is an 100+ hour a week job.  If he wants to save his marriage, then resigning from that job is not unreasonable (it’s hard to do while your at work).  On the other hand, if he wants to use this opportunity to divorce his wife and marry Ms. Broadwell… well, that would create a public relations nightmare if he did that while still Director of the CIA, especially if Ms. Broadwell is found to have committed a crime.  In other words, Patraeus might have decided to choose his personal life over his career, given the nature of the scandal.

Of course, I have no idea why he actually retired.  We may never know.  But the point is that just because we don’t know why something happened, doesn’t mean that it is the result of some presidential conspiracy.

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