Chrono Cross - The Scars of Time

If you can somehow do a branching storyline or multiple main characters then you can divide stories and content for many of the 40 characters between each storyline or main character.

Depends on what you can do with the event scripting system, I guess. If you can switch main characters and there isn't a "this person's death means game over" setting hardcoded for certain characters, then you're golden.

You could start with one character and have them find something that warps them to the End of Time, and from there have your narrator let you choose whose story to play.