Prefab doesn't work when placed in another scene.

I have a solid FPS controller and it works great. The only real difference between mine and the standard asset, is that mine has a "fake" model on top of it to show the players arms. I also have a script attached to it that has the same "WASD" keys to animations to simulate the character. I made a prefab of it and put it in another scene. All of the sudden nothing works, not even the standard Character Motor. Is there something I'm doing terribly wrong?