Crono and his party fight their way through the underwater Ocean Palace and eventually reach the newly relocated Mammon Machine, along with Queen Zeal, Schala and the mysterious Prophet. 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. After the battle at his castle in 600 A.D., the portal transported him here to the Dark Ages. Magus then attacks Lavos but he 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. Lavos' energy is so strong that it destroys the Kingdom of Zeal floating high above the planet. The remains of the Kingdom fall to the ocean below causing a huge tidal wave to wash over most of Terra Continent.