After Crono's party defeats Golem, they are imprisoned by Zeal, only to be rescued by Schala and Janus. The Prophet means to kill Crono's party, but Schala wants their lives spared. So they all travel back down to the Time Gate on Terra Continent, send Crono's party through it, and the Prophet forces Schala to magically seal the Gate for good.
After the Mountain of Woe fell, Schala arrives with Janus to Terra Cave to find Melchior and Crono's party. She tells them that she has turned her back on Zeal. But then Dalton arrives and kidnaps her to take her back to Zeal.
While the Mammon Machine is channeling Lavos' energy, Crono stabs it with the Ruby Knife. Energy is discharged and they all find themselves on a different dimensional plane where Lavos finally emerges. The monstrous Lavos easily defeats Crono's party and leaves them within an inch of their lives.
It's then that the Prophet reveals himself to be Magus in disguise. Magus then attacks Lavos but is also defeated.
Lavos then tries to steal the life force from Crono's party, Magus and Schala, while Zeal stands back and laughs. Mustering some strength, Crono tries another attack, but Lavos obliterates him, leaving no remains.
The party, Schala and Magus find themselves transported back to the Ocean Palace...without Crono. Before Lavos' energy destroys the underwater fortress, Schala uses the last of her power to transport them, and Magus, to safety.
Afterward, Schala was never found and believed to be dead.