Im a little slow so I am just catching up on this but on the 15 Nov Daily show Andrew Napolitano made a claim that the President KNEW about General Petraeus was having an affair BEFORE he nominated him to be the CIA director.  He based his accusation on his supposed knowledge of the FBI background investigative process.  He is full of it.  What he did do is preview the next line of attack now that the whole "fired for Benghazi" vector has failed.

First lets attack the base accusation - that the President KNEW of the affair before he nominated him.

General Petraeus was nominated to be the CIA Director on June 30, 2011.  That having been the public announcement one can assume a week or two prior all interested parties were informed.  No one is forced to become the CIA Director and since General Petraeus was well past 20 years required for military retirement, there was a normal process of "I would like you to be the CIA director." "Thank you Mr. President, I accept.  Do I have to retire from the Army?" (Director Hayden served almost 2 years before retiring so we can assume the President said he had to retire.) "Is there anything going on in Afghanistan that you need to finish or can you start soon?"  And so on and so on.  Bottom line, the President made his decision in Early to mid June, 2011.

By all accounts (so far) the affair between General Petraeus began AFTER he retired from the military in August of 2011.  Given the connection to Tampa/McDill/CENTCOM it is possible that some inappropriate relationship existed before but I personally doubt it.  Tampa/McDill is a fish bowl.  The presence of hundreds of foreign military personnel means there is a huge counter intelligence effort to ensure that everyone is doing the right thing.  Pulling off an affair in Tampa would be quite a feat and the behavior of the principles in this affair does not indicate they had the skills to do it.

Ah but Judge Napolitano claims that his deep knowledge of the background investigation process gives him special insight.  That might be true if President Obama had nominated General Petraeus to the Federal Bench, not the CIA.  

Investigations for judges are focused on two things  - criminal/embarrassing behavior and conflict of interest.  Obviously criminals should not be judges but "embarrassing" behavior is probably just as critical to Presidential appointments.  20 years form now being a star of ComicCon might be ok for a future judge but right now most Presidents would shy away from appointing closet Boba Fett to the Federal Bench.  Affairs as well as other sexual impropriety fall into this category - just ask Justice Thomas how tis goes.  Conflict of interest seems to get a pass from Republican Presidents but its still a big deal.  Strange investment patterns are a big red flag.  

Investigations for intelligence positions fall in two categories - Counter Intelligence (CI) scope and Lifestyle.  CI scope investigations focus on things that indicate your willingness commit espionage or vulnerability to exploitation.  Lifestyle investigations are just that - they look at your entire life.  As a Four Star General and senior Commander, General Petraeus has been through LOTS of investigations of both types.  By lots I mean lots.  His first, a simple criminal background check, came when he was appointed to West Point.  Next he would have had a National Agency Check (NAC) shortly after commissioning in order to receive a Secret clearance.  10 years later he likely had his first full CI scope background investigation for a Top Secret clearance.  Once he was selected for Battalion Command he would have had another more extensive background - just short of a full lifestyle check.  A few years later when he was selected for Brigade Command the same thing.  All through this time he would have done his normal Periodic Reinvestigations (PRs) that are required every 5 years.  Once he was selected for General Officer he had another deep look though still not as extensive as a lifestyle.  This is probably when he did his first polygraph.  After being selected for his 3rd star he would have gotten a full lifestyle investigation.  These are incredibly invasive and would have found any "exploitable" behavior.  Lifestyle polygraphs have no limits on questions like CI scope ones do.  Finally once he was selected to his 4th star and appointed as a Combatant Commander, he not only would have had an entirely new investigation but essentially been under constant "watch." We rely on "normal" soldiers to tell us if they see something unusual or are approached by the enemy.  For senior folks, we assign someone to do the watching for them.  When the President nominated him, I have no doubt that the people involved simply pulled the current "file" and saw there was nothing unusual.

The irony here is that once he became the CIA director he probably had fewer "watchers" and hence the "freedom" to have an affair.  No one is going to target the director of the CIA for exploitation.  Its the biggest of all big fish and truly an impossible task.  

So Judge Napolitano is full of brown stuff and ill-informed.  Not unusual for a Fox News star.  But we need to be aware of this new line of attack.  Now the President is appointing "corrupt" people.  He is putting someone in charge of intelligence who he can blackmail into lying.  And it not just him.  The Senate Intelligence Committee and the FBI are part of the conspiracy.  It is a baseless charge but one I think we are going to see evolve over the next week.

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