Skinner: You really have no idea who you're dealing with, do you? Mulder: I thought I was dealing with you. |
Mulder should really know better. But as is often the case Mulder just doesn't seem to learn his lesson. Despite this he was relatively well behaved in this episode as well. Of course being separated from Scully temporarily because of the case and not because they were shut down does eliminate a good number of opportunities for Mulder to act like a jackass.
Assuming he was only dealing with Skinner: Skinner's allegiances at this point are murky at best. The Cigarette-Smoking man was in his office the last time he had a face to face with Skinner. Why the hell would he assume he was only dealing with Skinner?
Accusing Skinner of being part of the cover-up: Even if Mulder knew for certain that this was the case it's probably not a good idea to openly say so to the man who could make things difficult for you at work.
Shouting at one's superior is also not a good career move.