That was just a theoretical explanation without fully closed logic. Just as the causality paradoxes in Final Fantasy XIII-2 cannot happen and though must be accepted with a grain of salt (and we don't talk about "fantasy-world so itc an happen" but a chain of events that is not possible through its axiomatic state of not being true and false at the same time, those things can only co-exist in theory). You do not need to worry about this, Chrono Trigger works with a multiversal concept and what did happen in one time line happened always on thar time line. If anything, Leene's vanishing would have meant another time branch and that is without Marle but the Marle we already have does not cease to exist. Right before the ultimate boss a certain character also mentions "this is one of many possibile realities". Not that I believe this works because it also has flaws but it is at least somehow imaginable. The story probably also mixes some things sometimes and makes mistakes but overall it is meant as Multiversal Time Tree. Later you can also do some things through time traveling and there probably mistakes have been made as only one time is shown all the time so it seems a bit like "things were changed" like for certain characters or locations. Actually those would be other times instead and not changed/replaced times.
It is such a thing:
The other branch should be "and Goku kills Cyborg Freezer" obviously.
So the only two things possible for time travelling are you "initiate" (or better "repeat") exactly the same thing on exactly the same timeline and were actually a part of that or you do something that was not a part of that timeline and this means another branch is a part of the concept. Both things happen in Chrono Trigger. The first thing with the saddest scene and the other one with almost everything else.
You will get to know where he is from and his time exists already.





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