Magus confesses to the party that used to be Prince Janus of Zeal, and that in the original timeline, he and the Gurus of Zeal were scattered across time by Lavos's awakening in 12000 BC. Stranded as a child in 600 AD, Janus took the title of Magus and gained a cult of followers while plotting to summon and kill Lavos in revenge for the death of his sister, Schala. Magus tried once more after the party's battle in his castle returned him to Zeal, where he disguised himself as the Prophet. At this point, Magus is either killed by the party, killed in a duel with Frog, or spared and convinced to join the party. The ruined Ocean Palace then rises into the air as the Black Omen, Queen Zeal's floating fortress. The group turns to Gaspar for help, and he gives them a "Chrono Trigger", an egg-shaped device that allows the group to replace Crono just before the moment of death with a Dopple Doll (doing so is optional, and the game's ending will change depending on the player's decision). The party then gather power by helping people across time with Gaspar's instructions. Their journeys involve defeating the remnants of the Mystics, stopping Robo's maniacal AI creator, giving Frog closure for Cyrus's death, locating and charging up the mythical Sun Stone, retrieving the legendary Rainbow Shell, unmasking Guardia's Chancellor as a monster, restoring a forest destroyed by a desert monster, and preventing an accident that disabled Lucca's mother. The party then enter the Black Omen and defeat Queen Zeal, after which they battle Lavos. They discover that Lavos is self-directing his evolution via absorbing DNA and energy from every living creature before razing the planet's surface in 1999 AD, so that it could spawn a new generation to destroy other worlds and continue the evolutionary cycle. The party slay Lavos, and celebrate at the final night of the Millennial Fair before returning to their own times.
