Questions raised (that aren't in the article):
1. Why do Gates sometimes lead to their other end and sometimes directly to the End of Time?
2. Who really caused the Ocean Palace Incident and other anomalistic distortions?
3. How does Lucca get the original version of Doan from ruined 2300 A.D. after defeating Lavos?
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1. Gate Ends
Inquiry
Until the party reaches the End of Time, Gates simply lead from one era to another. Afterwards, they mostly lead to the End of Time, though in one instance the Gates function as they did previously, taking Crono from 65000000 B.C. after the Tyrano Lair ruin to 12000 B.C. uninterrupted. Who controls how the Gates function?
Gaspar-Control Theory
GrayLensman
All time Gates naturally connect two points in time and space, but at times each travel destination may connect to the End of Time. Other than Spekkio, Gaspar is the only person who resides there. Since Gaspar is the Guru of Time, I speculate that he is solely responsible for Gates connecting to the End of Time, Conservation of Time theorem nonwithstanding. He arbitrarily decides if and when Gates will connect to the pillars at the End of Time. He may also have to witness a Gate used in order to acknowledge it and link it at the End of Time.
2. Who really caused the Ocean Palace Incident and other anomalistic distortions?
Inquiry
Four anomalistic instances of temporal distortion occur in Chrono Trigger. Firstly, in the Ocean Palace Incident, strange Gates materialized and gated the Gurus and Janus to various eras across time (and in the new timeline with the Prophet, one would gate Schala to the Darkness Beyond Time). Secondly, Marle's pendant reacted with the Telepod to take her to 600 A.D. Thirdly, Magus's summoning Lavos in 600 A.D. caused a raging temporal distortion that sent Magus to 12000 B.C. and Crono's group to 65000000 B.C. Third, after Crono was at the new Ocean Palace Incident, Schala fell into a dimensional distortion that took her to the Darkness Beyond Time. Last to occur is the new Melchior and Janus's disappearance from 12000 B.C. Who caused these, and why did, in each case, important individuals conveniently go to important eras in the planet's history?
Theories
Entity Plan and Error
These Gates were all effected by the Entity, whose first action to save itself occurred in 12000 B.C., when it gated Janus and the Gurus to the important eras of its lifetime. Secondly, it created the Gates, the one at the Millennial Fair included; once it had found its savior, Crono (as evidenced in the instructional manual, which references "guardian spirits," probably a translation quip, as choosing Crono), the Entity then caused the Gate to open at the Telepod exhibition and start Crono on his quest. Lastly, though Magus's summoning Lavos was the cause of the temporal distortion at his lair, the Entity had a hand in sending the affected individuals to certain eras. If the Entity can create stable wormhole Gates through time, it is not a cop-out to believe that it can usher its own plan along by having an active hand in these instances of time travel.
That said, it is probably not the Entity's doing that Schala was taken to the Darkness Beyond Time through the dimensional distortion in the second Ocean Palace Incident. Whether the planet is aware of Belthasar's Project Kid is debatable, along with whether it even perceived a threat in the form of the Time Devourer, which may have been outside the realm of its perspicacity. Sending Schala to a place where she might evolve with Lavos into a being that could devour time is certainly not in the interests of any reasonable entity, however.
Finally, concerning the disappearance into black Gates of Melchior and Janus in 12000 B.C., this is thought to be an example of the Time Bastard theory in action. (I'll link this in the theory entry)
3. DOANLOL
Inquiry
After Lavos is defeated, the future should instantly become pretty and beautiful, and the ruined future timeline should disappear. This includes Doan, the old man who led the Arris Dome survivors. Yet Doan is brought by Lucca after Lavos is defeated to 1000 A.D. for the Moonlight Parade. How did Lucca pull this off if Doan should no longer exist in his old form?
Theories
Preplanning
Lucca, in a show of optimism, previously arranged for the ancestors and descendants of the Guardia line to show up at Guardia Castle. This would sadly cause a complete breakdown of history like the [[Guardia Line Paradox]], resulting in a history absent of Marle's ancestors (meaning Guardia wouldn't even exist). The only loophole that could work is if Lucca only took Doan out of the future and gathered the other relatives only after Lavos was defeated. This is quite a stretch, unfortunately.
Misconceptions
Different Doan
The Doan we see is simply the new Doan. However, this theory is flawed because Lucca wouldn't have brought him back otherwise, and Doan also notes that Crono and the team gave him hope, implying he previously did not have "hope" in the ruined future.