Here is the very rough draft.
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Somehow, King Zeal becomes the Arbiter of the Frozen Flame and discovers a Time Egg, allowing him (as detailed in Radical Dreamers) the ability to travel anywhere in time. In 1002 A.D., the heroes of time have not seen their friends for awhile, and are more concerned with the mobilization and industrial revolution going on. Time begins to change, and the heroes end up in Chronopolis as a prototype of the Porre cyborg program tracks them. As time continues to change, the heroes strive to set things right under the watchful eye of Belthasar, visiting various eras while crossing paths with old enemies and the Porre cyborg. Eventually, time is completely rewritten from 65000000 B.C. onward, resulting in a completely new world the heroes find themselves in.
They explore this new world and eventually make it back to prehistory to set things right; however, in the future of this new world, its own version of "Chronopolis" detected the heroes' presence and dispatched its own time travelers. As the heroes get their bearings after restoring the world, the new group is completely baffled to find a world new to them. As more of the truth is unraveled concerning King Zeal, things come to a head in 1002 A.D. and other eras, with the party confronting the group (who feel the heroes have committed genocide upon their world) and the Porre cyborg, who slowly regains his humanity. Once the root of the problem is diagnosed, the heroes set out to find King Zeal and eliminate his influence over time, leading to a climactic battle in which Schala (previously located and rescued) is lost to the Darkness Beyond Time and perhaps other fates befall the heroes.
At the end, the themes that changing time is vastly dangerous and potentially world-ending, that utter determination to set things right can ultimately prevail, and that fundamental differences between peoples can perhaps be reconciled (Porre vs. Guardia, Mystics vs. Humans, Humans vs. Reptites) if the parties are contrite and ready to meet each other will be reflected upon.
Possibly, it will be revealed that Belthasar caused the entire mess in a botched attempt to revive King Zeal with the Time Egg, as Belthasar and the King were excellent friends and Belthasar wished to meddle in time to bring him back to the future. Perhaps the effort backfired, leaving King Zeal in possession of a Time Egg and perhaps the Frozen Flame, used to power Chronopolis but ending up with King Zeal after the failed attempt. This would give Belthasar necessary justification for going a little mad and also wishing to finally set things right with Chrono Cross by nullifying the Time Devourer, which at this point would be in its infant stages at the Darkness Beyond Time.
Conflicts
Mystics versus humans, who try to find common ground after 600 A.D.
Guardia versus Porre, who believe Guardia is foully corrupt and has most of the world's wealth tied up in excess, and would embrace a form of socialistic militarism in rebellion.
The Time Travelers of the "Other World" who find Crono's world and try to change it back, though Crono cannot let them -- who is right in this situation? What morals apply to time travel?
The humanity of the heroes versus itself. Lavos's influence is pervasive, having evolved humanity and now acting somewhat through King Zeal to change time. Can the heroes find faith in humanity? And robots!
Humans versus Reptites and other pre-Mystics, who struggle to find heat and food in the cold, new world of prehistory, and hate the warm-blooded ones for their ability to naturally adapt.
Belthasar versus himself. He knows many things about history which he chooses not to reveal to the party.
