Hmmm...So if they're doin' their story mode along the lines of how Netherrealms did MK's, I believe we'll see a bunch of different chapters, and play as a different character for every chapter. Then the Arcade Mode is where they'll be personal, non-canon endins' for every character. Personally I think this is a great idea because this'll organize the plot for games to come, and we won't have to figure out which endin's are canon, and which aren't.
About the "Raph=Nightmare" theory, I really can't see this bein' true. I mean, I always thought Raph was always on the evil side from the jump. He has always wanted the SE ever since his inclusion in SCII. Also, I think he's too strong willed for the SE to take over and control him. I think if he ever got a hold of it, He would still be sane and the SE would take a form to the weapon of his choice [Rapier] like it did with Cervy when he wielded it, not the other way around. Finally, there's a big difference between SCIII-IV Nightmare and SCV Nightmare, and that is the SCV one has a person inside of it. And seein' that both Raph and this person-full Nightmare are in the same game, separated from each other, and with completely different styles, I think it's say to assume that they're not the same person, but hey...I've been pretty wrong in my beliefs before [*cough-Sophiemaretheory-cough*]. I actually think that the person inside Nightmare could be Kilik, but I also think it could be a completely new character, altogether. We'll se once the game's released, I guess....
