It depends on if you mean going back and fourth in Crono Trigger or if you mean go back to times you previously were at in the game. Either way you can using events and variables.
If within the story line I would suggest just using variables for story progression and have it so that a lot of events are based on those few variables so when they go back everyone will act as if they didn't get to point "x" yet. For things to be better you would have to do a lot of work and save several variables positions in one variable (I think you can do that)
Crono Trigger would have more events needed for each specific action done in the past, but because you wouldn't ever undo actions it should just be like normal variable use, just with copy/pasted maps of everything.