Themes
1. Time can be changed, most importantly in the present
2. Reconciling differences for peace (Reptites v. Humans v. Mystics)
3. Time should only be manipulated by those with extreme morality and responsibility (basically a sort of potshot at Belthasar as he is in Cross)
Overarching Plot
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.
Group 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.
Personal Conflicts
Crono - Crono will deal with taking on responsibility as the true hero and new king of Guardia. His main conflict is comparable to Vash the Stampede's; he will be frustrated by the seemingly repeated failures of not being able to change time to the way it should be, or angry that he couldn't save EVERYONE in a bad situation, etc.
Marle - King Guardia XXXIII dies during the course of the game, leaving Marle to be a full fledged regent. This will damage her bright idealism somewhat, as she'll now have a front row seat to the problems troubling the world of 1002 A.D. She'll also have to cope with her father's death.
Lucca - Lucca will be the voice of the moral applications of time travel, questioning Belthasar at times and also receiving much development during the New World arc. She'll also struggle with not being able to join the future fully, as her place is in 1002 A.D.
Robo - Robo may be involved a short arc about robots being an extension of or an improvement over the Lavos-evolved humans. Only Robo will be able to understand on that level (since humans aren't aware they evolved from Lavos), but robots will still find conflict as they have a natural pride in their superiority compared to foolish, rampant humans.
Glenn - Glenn will deal with the concept of honor, the problem of finding common ground with the Mystics, and the issue of wanting to do much to change the future for the better in 602 A.D. but being restricted for fear of altering it too greatly. The Vanguard's zealousness will be an issue for him; he'll realize it may not have been the greatest idea. We're going to use the real Glenn here, not the person Woolsey made him out to be. The real Glenn was sort of a hardass, down to earth guy.
Ayla - Ayla is at the forefront of the symbolic death of the prehistoric way of life due to the coming Ice Age. She will eventually decide that surviving the cold will be a great test of her strength and the courage of her people.
Magus - Magus will be wary of accepting King Zeal as his father, and will blame him for everything going wrong initially.
Villains
King Zeal - King Zeal died originally, but was nearly resurrected by Belthasar, who used a Time Egg in conjunction with the Frozen Flame to revive his old friend. King Zeal resultingly came into possession of a Time Egg and the Frozen Flame, becoming its Arbiter and subject to Lavos's impressions. King Zeal then began whimsically changing history, eventually becoming flabbergasted at the cancellation of his changes by the heroes, and seeking to do them in. He's fueled negatively by Lavos (like Queen Zeal), and uses time travel without reason or morals.
Other World Time Travelers - Cakulha, Coyopa, Yaluk (leader, female) - They seek to return the world to the one they came from (Tohil), and see the heroes of time as genocidal murderers. They utilize a device called the Alom to travel through time, though travel is limited as the Alom must recharge. They mess around the prehistoric era before confronting the group in another time period. Lastly, they find King Zeal and get in league with him for a plot to lure the heroes out, finally dying at the hands of the heroes. Their names are references to lightning gods of Maya; their "Epoch" was a Mayan sky god name.
Porre Cyborg Protoype X-14 - He is the first working cybernetic human created by Porre, and is sent as a spy and assassin to Guardia. He witnesses the time travelers depart to 2300 A.D., reports his findings, and is given the instruction to kill Crono and the others. He shadows the group and stows away on the Epoch, making it to Chronopolis virtually undetected, where he downloads more information. When the party returns to 1002 A.D., he goes with them via the Temporal Dispatch Chamber. The change in time in 1002 A.D. is later blamed on him, and the party thinks he is responsible for changing time for a while. He is later stranded in the new world; he initially tries to kill the party but realizes they will resurrect Porre by changing the world back. The experience breaks his ties to Porre, and he eventually sacrifices himself.
Era Villains
Zavra - Zavra is the leader of the remaining Reptites, and lives in the last Reptite hideout.
Dalton - Dalton continues to research immortality in 12000 B.C., using any spare scrap he can find from Zeal. He eventually gets in league with King Zeal as a shot for immortality and revenge against the heroes.
Kasmir - Kasmir is a forerunner to the Heckran in CT, a sort of miscreant that likes stirring trouble and tries to revive Mystic hostilities. He's relatively unpopular until a tumultuous event causes many to find faith in his views.
General Montcrief - General Montcrief is the bored leader of the Porre army, who clamors for action and exercises little restraint.
Proto 5-02C - Proto 5 is the latest Proto design, and Proto 5-02C is the first complete robot of its type. Only two others have been made. Due to advanced AI and processing capabilities, Proto 5-02C has emergent intelligence and wishes to establish laws, freedoms, and an identity for metallic creations. By accident, he learns of Chronopolis, and demands to know more, creating a public storm in the process and threatening the security. His main argument is that if Chronopolis is capable of temporal exploration, humans are extremely ill-suited to be the ones doing it, and that they put all of history at risk by allowing their imperfect influence to spread. Belthasar authorizes a special mission to terminate Proto 5-02C moments after his creation, which causes all sorts of moral objections from the party. Ending for this character is pending. I suppose he's not really a villain.
The Shocking Occurrence
At some point, the team will suffer a great failure and others will perish because of it. During the resulting chaos, Magus, Robo, Glenn, and Ayla are all subject to bad magic, making them much more draconian, negative, and chaotic. The story will switch to their perspective as they recklessly travel through time causing destruction for their own selfish ends. They will eventually snap out of it, but not before Crono, Marle, and Lucca have had to correct their mistakes.
Additionally, at some point the party will have to choose between saving time and saving a person. The first time they choose, a feedback loop is caused.
Prologue
