That was amazing Boo the Gentleman Caller, you really captured the spirit of Masato Kato's storytelling in your planned sequel. I especially loved the idea of a broken Schala living in a self-created deluded universe. (because that is something she would definitely do) and a very powerful story beat to see play out.
Thanks. I tried to envision something that captured the spirit of Chrono Trigger, but still added some of the more complexity of Cross.
The main concept is rather great, I enjoyed the idea of a Lavos failsafe gathering power and managing to resist the pull of his fate, though I am not sure how Schala would play into helping him resist this. I suppose since Lavos and Schala did share a symbiotic relationship for an endless amount of time this feeling may have manifested into a desire for ?companionship? in the main Lavos host. I am a little confused about that aspect.
In my story, this dream world literally exists as a giant blue sphere of pulsating energy in the ice age. It's there because, after all was said and done, she decides to try and spend her energy on helping the people of her own era, but once she arrived there, her willpower was sapped and she sank into a deep depression, ultimately choosing that she would rather live in a false, perfect reality rather than the real world.
So in my envisioned plot, you actually have to travel to Schala's false reality / dream world twice. The first would be about equivalent to when Crono and company first visit the End of Time in Chrono Cross. The first time you travel there is for intel and to ask Schala to join the heroes at the Time Research Laboratory with Balthasar; she gives the first info dump about why the Chrono Cross reality no longer exists, and she reveals that the Serge of Chrono Cross was ultimately destined to become an Assassin of Time. She refuses to join the party, but does feel a kinship to Phase for the exact reasons you describe, although she doesn't recognize it -- she was bonded with Lavos as the Dream Devourer in the Darkness Beyond Time, and Phase is a sort of semi-manifestation of Lavos. Phase feels drawn to Schala, as well. I also envision a hint of attraction.
Throughout the story, Phase would think about Schala often. He pities her, but he also mentions wanting to help her.
Later, the party returns to the false reality of Schala and is able to snap her out of her reverie. In fact, it is only because of Phase's motivation that she can move forward and face the reality. She joins the party, and for the rest of the game, the two bond. Later, when Phase learns that he is just another destined Assassin of Time, Schala resolves to save him, as she couldn't save Serge.
The party spends time trying to stop Phase, but we ultimately realize that their attempts only hastened the process. In 3 million BC, at the moment when mankind first encounters the Frozen Flame, Phase absorbs the last pieces of energy needed to ignite the transformation into the Assassin of Time. It happens biologically -- his physical body literally begins to blister and transform (think Akira meets a Star Craft Zerg), and Schala pleads with him to save himself. Unfortunately, Phase has no control over the process and literally can't stop himself.
As a sort of fleshly cocoon-pod begins to form over the transforming Phase, the final stage of the transformation, Schala leaps into the pod and momentarily merges with Phase. The two are trapped within the pod, and the party laments that they've failed in their mission; Phase has evolved into the Assassin of Time and will soon rejoin Lavos, and Schala with him (assuming she even survived). However, the pod breaks down, revealing a perfectly fine Phase and Schala -- her willpower (and experience as having been previously linked to Lavos) allowed her to save Phase.
Meanwhile, a time-traveling Dalton has observed this, eventually leaps into the pod, and becomes and incomplete Assassin of Time with the goal of becoming a god - becoming Lavos. He is ultimately the big bad for the final act of the story.
All in all, it is a wonderful story and may just need a little more refinement. You said you planned it for it to be a Chrono Trigger hack at first, with 7 (perhaps 
character limit I guess that would be...
Phase, Roba, Ada, Crono, Marle, Glenn, Schala?
I envisioned it as a cast of 9.
-Phase is first, and he is quickly joined by his rival and a descendant of Toma from 1200AD.
-They then meet a time-traveling Robo on a mission for Balthasar, and the three join up.
-They then travel to 2300AD and Ada joins the team.
-Later they gain Marle in 1005AD.
-They would then get a new character, a Reptite and the daughter of Azala in ~65 million BC.
-After spending a chunk of the story trying to save Glenn (which is why they had to return to 65 million BC), they would save Glenn, turn him human, and he would join the party.
-I hadn't fully decided on the other new character, but I was picturing a returning Chrono Cross character who was from Zenan mainland and thus not part of the erased Chrono Cross timeline. I had considered Zappa (who would be a much younger man) or better yet, a teenage Norris. I had also considered a character from 3 million BC; perhaps one of the first people to learn magic from the Frozen Flame?
-The second-to-last character would be optional, who would be Crono.
-The final character, equivalent to Magus, would have been Schala.
I am not sure on the idea of Rouen though. Since I can't see how someone who wants to undo his crazy dad's machinations would become the embodiment of disruption and destruction.
So I had a complete first draft of the story that is pages and pages long. Rouen doesn't even exist in the second draft, nor is there any exploration around counter-time, so I admittedly never fleshed out how he would work or fit into the story. In my mind, Balthasar is sort of a control freak - he wants to master time. Look at Chrono Cross and his almost god complex with the complexity of orchestrating Project Kid. Even though the version of Balthasar we meet in my story is yet another version of Balthasar, this version maintains that same desire to control. Thus, his son was envisioned as a counter. Where Balthasar wants to meticulously control and manage for an optimal outcome, his son would be chaotic, driven by anger (or insanity) and want to destroy. This was written years ago, before the new Star Wars trilogy, but I picture Rouen being akin to Kylo Ren in his dynamism.
Finally, didn't Crono already send the original future to the Darkness Beyond Time? Why would he feel conflicted and not choose to save his own era? I suppose Phase could try to stop him because of those he knows in 2200 AD and could realize that they would also be destroyed by stopping the Fall of Guardia.
Well, the note from Lucca in Chrono Cross mentions that they never considered the negative fallout of their efforts until after the events of Chrono Cross. They just thought they would destroy Lavos, save the future, and that would be that. I don't think they considered the moral implications until much later.
In fact, what you mentioned in a part of the story. When Marle joins the party, they intentionally try to hide the fact that Guardia is going to fall in a short time. Phase, who was studying history and the fall of Guardia, wanted to tell her, but Balthasar and the others essentially force him to keep his mouth shut. If they should stop the fall from happening, there will be yet another 2300AD timeline, and in that, it is possible Balthasar won't have his Chronoscope (invented in this timeline) to monitor and police space-time.
Later, when she finds out she goes ballistic. She actually leaves the party before eventually recognizing that the threat of the Assassin of Time is far worse than the fate of her kingdom. She does promise that she'll save Guardia however necessary once they finish their quest.
(A note about Marle's characterization in my story: Crono and Marle are engaged and to be married. Crono is undergoing training and is a retainer for the King, trying to learn the ropes of his future royalty. He is super serious about it and very focused. Marle, on the other hand, is wanting to settle down, raise a family, and she is still considering whether or not she is capable of the responsibilities of wife/mother/queen. Thus, Marle and Crono are somewhat at odds; Marle is shirking her duties, while Crono is almost embracing them too much).
The war between Porre and Guardia begins during the story I plotted, and I went back and forth on how much to explore of the fated battle at Guardia Castle. If you remember, I mention that Dalton has the Forge - Melchior's artifact that grants him control over dreams and life. This is what allows him to possess the Masamune and corrupt it, and it's his control over the Masamune that allows him to destroy Guardia.
One of the first missions the party has in the new 2300AD is helping Lucca and Ada retrieve the Frozen Flame for their lab, as they needed it to power the place (sort of echoing Crimson Echoes). It lays at the bottom of the ocean floor in the ruins of the Mammon Machine, so there would be a dungeon to retrieve it. It would then be installed at the Time Research Laboratory and would power it. You would later learn that Balthasar can use the Frozen Flame (completely under his control using annihilation energy) to create a sort of space-time anomaly around the lab, making it exist in a pocket dimension.
I ultimately figured that events would explore the party stealing the Forge from Dalton in 605AD. Without the Forge, he would never be able to raise Porre up into the powerful nation it is, and he would never be able to destroy Guardia. Crono and Marle would ultimately decide to save their history and allow the multiverse to take care of the rest. After all, we'd learn that the Darkness Beyond Time doesn't actually hold discarded/erased timelines, only echoes of timelines created via time travel. Thus, no time timeline is ever erased, only new timelines can be created.
In game we'd see Porre shrink from a mega cityscape into it's more traditional form as seen in Chrono Trigger. You'd also learn that the fact that the Time Research Lab exists in a pocket dimension outside of space-time makes it exist despite further timeline changes.
I sort of did that so this version of Balthasar would be the last (from a story perspective). Constantly rewriting history and creating new 2300AD - and new versions of Balthsa - would be lame.
Poll