After having jumped through the Time Gate in the Lair Ruins in 65,000,000 B.C., Crono and his friends find themselves in a new era. It's 12,000 B.C., known as the Dark Ages, where a magical kingdom floats high above the surface of the frozen planet.
Traveling through Skyways and Land Bridges, they make it to the floating kingdom where the people there, calling themselves the Enlightened Ones, are able to use magic. In talking to the people, Crono's party finds out that Queen Zeal is channeling Lavos' power through the Mammon Machine. Knowing that Lavos is the root of the inevitable destruction of the planet, they want to put a stop to Zeal's plans.
They learn that Marle's pendant was actually Schala's pendent in this era, and it's a magical pendant that can be powered up by the Mammon Machine. So they power up the pendant to use it to enter the Queen's chambers. As they enter, the mysterious Prophet warns Zeal that Crono can be dangerous. So Dalton sics Golem on them.
After Crono's party defeats Golem, they are imprisoned by Zeal, only to be rescued by Schala and her kid brother Janus, who know what their mother, Zeal, is doing is wrong. The Prophet means to kill Crono's party, but Schala wants their lives spared. So they all travel back down to the Time Gate, send Crono's party through it, and the Prophet forces Schala to magically seal the Gate for good!