I think they touch upon that in Chrono Cross, but I could be wrong (I haven't played it for almost a decade). I do remember that one of the main plot points is that Crono and friends' meddling with time to defeat Lavos caused alternate time-lines/dimensions/whatever (ie: a time-line where the reptites won). Heck I think the Dead Sea or whatever its called in the game is where you learn about it from little "ghosts" (for lack of a better term) of Crono, Marle and Lucca as kids.
But then again, I haven't played the game in almost a decade and my memory is spotty at best. (and to get back on topic...)
In the first Ninja Turtles game on the NES, when one of your turtles "dies", he demutates into his normal turtle form/whatever. However, its possible to find them, fully mutated, and tied up in certain areas that the Foot controls and save them. My question is, if they demutate when defeated, why would the foot remutate them instead of leaving them be or simply killing them, their worst enemy, in a weakened state?