Mulder had been played for a sucker for far too long to put up with it anymore. CSM was going to get what he deserved and Mulder was determined that it would be him delivering the punishment.
Mulder didn't want to be a fool for this conspiracy and longer. He didn't want to be an idiot who accepted what he was told without question and followed their lead.
He was glad that Scully was with him on this; it made it a little more bearable. But they should watch out, because he wasn't taking it anymore.