I've been slowly working my way through this thread again. Have thoughts that seem a bit worthwhile to me (after twenty pages of reading). Sorry if some of this is already resolved but...
Eclipse Magus- I'm strongly convinced that he is post-Trigger Magus. Not Magus from some alternate dimension or something weird like that. While it is worthwhile to test all options in a game, including visiting Time's Eclipse without having recruited Magus on the North Cape, the recruitment seems to me to be the canonical event in the game. Specifically because of this: "If so, hello, Janus!" I don't think Lucca would write a letter to Kid speculating on whether or not a guy she helped whack caught up with Kid. Its almost a minor plot point (I don't think anyone really wants Magus dead in the plot), but if the canonical ending is that Magus survived to search for Schala, then some version of him suddenly finding Schala seems logically like it would be him, Prophet garb or not. I think even the attitude fits in. He did not seem particularly hard of heart. He was never really chummy with Crono and Co., even though he helped them revive Crono and fight Lavos. There was no tearful farewell at the end of the game. He did his loner thing and mutely entered the Gate to continue his journey and find Schala. Crono wasn't his concern anymore and I think its only natural that the next time he sees them (probably feeling close to success again), he reacts with coldness. The first time he met them, they screwed up his summon. Sure he fails anyway (either by being eaten or whatever), but he'll always have that loving memory of them bursting in to mangle everything.
I think in the end, he was simply burned out. People react to his dialogue leading up to the loss of his memory with surprise, but its really not that weird. He spent his life, fueled by hatred for a creature that took away everything, particularly his family and his loving sister who, though his mom lost her mind, always tried to protect him. He finally manages to destroy said creature and then goes through time to find her. Finally finding her, going through what must have been all kinds of Hell to get into the Darkness Beyond Time, she rebuffs him and tells him to stop. That all of his efforts are pointless.
His life has been lived for that moment. I think despair is a natural reaction.
I don't think Amnesia Magus is Guile though, and I don't see why everybody started speculating that he was. It's clear that he wasn't. It was stated explicitly by the creators. He may have been intended to be Guile, but the idea was scrapped. So Magus is still unaccounted for. Though he has amnesia and is searching for something he's unaware of. Fun story ideas for that one. Along with whatever else happened to Crono and Marle (who are probably dead, though I'm leaning toward them being in hiding).
