After acquiring their magic powers in The End of Time, Crono and his party return to 1000 A.D. only to find themselves on the Eastern continent that is inhabited by human-hating monsters calling themselves Mystics. In talking to the monsters living in Medina, Crono and his party find out that Magus summoned the destructive entity Lavos back in 600 A.D. to destroy humanity.
In traveling north, they find the Forest Ruins where a magical pyramid stands amid the trees. They have no idea what it is. Traveling west, they come across Melchior's Hut where they find Melchior, the swordsmith Crono and Marle met back at the Millennial Fair at Leene Square. He tells them that they can reach the Northwestern continent by going through Heckran Cave.
Heading into the Cave, Crono and his friends battle strange monsters and eventually find a magical pool of water that transports them to the Vortex Pit just east of Lucca's house in Truce. After paying a quick visit to Taban and Lara, as well as Crono's Mom and Fritz and Elaine's Market, the party enters the Time Gate at the Millennial Fair, transporting them back to The End of Time. From there, they take the Gate that leads back to Truce Canyon in 600 A.D. on a mission to prevent Magus from summoning Lavos.