X-Men: Episodes 11 and 12
Days of Future Past: Part 1 and 2
Well, this was just confusing. It turns out that Mystique is Rogue's foster mother after all in this show. She was working for Apocalypse because of... reasons.
I got a strong Terminator sort of vibe from these two episodes. If the unstoppable killer in the form of Nimrod wasn't obvious enough, then the general timey-wimey tone should convince you. Then there was the music which seemed like it was ripped right of the movies. Wolverine even referred to Bishop as a Terminator. There was no way that this was an accident, the people that made these episodes must have known what they were doing.
I think there were suspicions of Gambit being a traitor in the comics as well. It turned out the traitorous X-Man was Professor X because he transformed into Onslaught or something. I'm not sure myself, it was all very confusing. Something about the dark side of Professor X's mind melding with Magneto... I think. Comics, eh?