From the back of the box:
The millennium. A portal is opened. The chain of time is broken. A young man is transported into the past, altering the course of history and the outcome of the future. He has to find his way home, but first he must travel to the outer edges of time to repair the world's chronology. On the way, he encounters strange friends and foes, utilizes incredible devices and vehicles, and penetrates and neutralizes the fortresses of the past, present, and future. A paradox has been created. If he does not restore the order of time, nothing will ever be the same. He is the one who will become a hero. He is Crono.
Chrono and friends must use time itself to rid the planet of a powerful and horrible force that stands to destroy the world in any and all time periods.