So the story took on a more political theme and showed how villains often see themselves as the heroes and vice versa. There was a lot of subterfuge and we based a lot of the game on unused elements from Crimson Echoes. Although we didn't directly rely on Crimson Echoes, we did make sure the plot elements fit (such as subtle references to King Zeal and the Atash Kadah, amongst other things).
The plot followed Norstein Bekkler, who was a teacher at a magic-based place of learning in Zeal, his younger brother (and a student at the school), Wellsville, as our protagonists. Long story short, they meet up with an Earthbound man named Wazuki and several other characters and get involved in a cold war involving Zeal and another isolationist nation called Calaspera that has closed itself off on the ocean floor.
Early on, Wellsville is accidentally killed by agents from Calaspera. Norstein pledges himself to Queen Zeal and vows revenge, and he subtly manipulates the party to help him stop Calaspera. It takes the party nearly 1/2 of the game to get to Calaspera, but once they get there they realize that Calaspera are actually the good guys and Zeal are not as good as they seem.
A short time later, Norstein's betrays the party and accuses them of being enemies of the state for turning their backs on Zeal. We also learn that he has been aiding the Queen to try and manipulate magical genetics, essentially furthering the genetic magical traits of the Zeal citizens (and further subjugate the Earthbound) using the a captured Frozen Flame.
Norstein's research bares some fruits, which indirectly creates the Mystic race as seen in Chrono Trigger. Later, Norstein himself interfaces with his machines and his body is torn asunder, rendering his face and hands from his body.
We then learn that the two nations of Zeal and Calaspera are descended from those who first came into contact with the Frozen Flame in 3 million BC. One sister founded Zeal, the other founded Calaspera. Both earned immortality and near-godhood by their contact with the Frozen Flame and have secretly been in a cold war for eons. Zeal and Calaspera have risen and fallen in multiple cycles, and the current incarnation of the countries we see are actually the seventh such iterations of the civilizations.
The two sisters - viewed as religious icons by the citizens of each country (as seen by the goddess statues in Zeal as seen in Chrono Trigger) are then tracked down and killed by Norstein, their powers used to help raise Zeal into the sky and crush Calaspera.
Although the heroes cannot stop Norstein and Queen Zeal in raising Zeal out of the ocean, they are able to stop Norstein, who by this point has been possessed by a dark creature called the Black Wind - a literal conscious universe that feeds off of death and destruction and plans to use them Frozen Flame to destroy our world and use it to feed itself.
Calaspera is finally defeated by Zeal, and it's ruins at the ocean floor are later re-utilized to become the Black Omen.
Meanwhile, the party members, the Gurus, and the leader of Calaspera (who is essentially a fourth honorary Guru) use Calaspara's secret prototype weapon - the Chrono Shift. It is revealed to be an experimental device that can shift time and lock it away in a temporal loop.
The heroes storm Zeal's Elemental Palace, where Norstein Bekkler (possessed by the Black Wind entity) readies to harness the Frozen Flame for nefarious purposes. They are unable to defeat it, so instead use the Chrono Shift to lock it away for eternity in a time paradox. To do so, however, they are forced to sacrifice themselves.
Some of them are locked within the temporal loop along with Norstein. Wazuki are his pregnant wife Marge are the only ones to escape, but are thrown into the far future, where we later meet them as characters in Chrono Cross.
After centuries within the temporal loop, Norstein is able to manifest his arms and head and floating entities, but he has been driven mad and seeks only entertainment...
That's essentially the super condensed version.
