In the year 1000 AD a town named Leene's Square, a young swordsman named Crono dwells. He wakes up and goes to the Millennia Fair. Inside the fair he bumps into a girl named Marle. But little did Crono know, Marle is really Princess Nadia, disguised as a normal girl to have fun at the fair. They both explore the fair and go to a science exhibit hosted by Crono's friend Lucca. Lucca shows off with her

father a time machine. Lucca asks for a volunteer to test it out. But everyone was too scared to go but Crono volunteers to try out the machine. Marle, who was fascinated, wanted to try the machine too. But when she stepped on, her magical pendant reacted to the machine and warped her into the past leaving the pendant in the present.

Crono, being brave takes the pendant and goes off to save her. But as time passes, more and more tasks await them to save the past, present, future and the end of time.