What kind of game do you want to make? Maybe you can start with mechanics you want to implement and incorporate time travel into the story. Or go the other way, write the story you want (with time travel of course) and integrate it into the game mechanics. Rewinding like Braid is hot right now I think. Swapping between different "time periods" within one level to reveal differences and make progress is another mechanic. Chrono Trigger used this.