Redux

Mulder:  There are those who can be trusted.  What I need to know is who among them is not.  I will not allow this treason to prosper, not if they've done this to you. Scully:  Mulder, we can't go to the Bureau making these accusations. Mulder:  No, but as they lie to us, we can lie to them.  A lie to find the truth.

And so Mulder asks Scully to lie to the authorities about the body in his apartment.  Mulder doesn't ask for much does he?

General Punkesque Behavior

I understand that he was trying to save documents that Ostelhoff was burning but I don't think that knocking over a garbage can with flaming refuse in it is a good idea.

Scaring Scully by hiding in her darkened bedroom.  Surely there had to be a better way to hide out and still get in touch with Scully.  Perhaps a note from the Lone Gunmen would have done nicely.

Asking Scully to lie about the body on the floor of his apartment:  If his scheme hadn't worked he would have dragged Scully into the same doo doo that he would have been in.

Mulder will never be mistaken for James Bond.  Randomly trying doors just screams "I don't belong here!"

Criminal Activity

Homicide:  Granted it was justifiable but the subsequent cover-up can only make things look fishy.

Obstructing Justice:  That whole lying to the authorities thing.  While Mulder didn't actually lie to them as he hadn't spoken to them staying hidden and playing dead while having Scully lie to them certainly makes him as complicit.

Trespassing:  Sneaking into the Pentagon by impersonating Ostelhoff will definitely get Mulder on the government's shit list.

Theft:  Stickyfingers!Mulder strikes again.  No matter how well meaning taking the vial from the Pentagon of all places without permission is still theft.