Well, it's a minor spoiler, but if you really want to know why...

Towards the end of CC, Kid recieves a letter from one of the characters from CT explaining a bunch of plot elements, but also creating a ton of other questions in the process. At the end of the letter, the author says something like "I know you'll be safe because 'He' is there to protect you. P.S. Janus, if you let anything happen to her, I'll kick your ass."

That little "P.S." suggests that one of the characters in the game is actually an alternate-future version of Janus. The two big possibilities are that it's either Serge or Guile. Serge, because the reference seems a little too important for it to be any of the side characters. Guile, because it would more logically fit with the story of the game. Either way, it's not Magus, it's a grown up version of Janus, only if he took a different path than the one that lead to him becoming Magus. Did that make any sense?