Sidequest:
As part of the round of sidequests before the plot gets back on track to rock the final boss, Magus will get disconnected from the others by a catastrophe in order to undergo some plot development. He'll end up on a desert island, El Nido size, off the coast of the Medina continent. Due to his wounds, he'll be forced to wear normal clothes (I'm hoping that Geiger figures out controlling NPCs at this point, so we'll have a Magus (commoner) sprite) and help the few Mystics there who fled during the war and have been making a living. He'll be initially dismayed at losing contact with Schala again, but the place is peaceful, and for the first time in his life, he can rest. The Mystic villager periodically speaks with him about the war prior to 600 A.D., and learns of Magus's true history. The player will learn some fabricated history about the motives of the Mystics in the war and other stuff.
This'll be 80% of the sidequest - gentle development. The rest will come when marauding Mystics from the Medina mainland want the islanders to rejoin them in an army and bear weapons once more. Now, the Magus from Chrono Trigger might say "well, sorry guys, but this is your business, so SEEYA" and let the islanders be overpowered, but the objective here is to show that the emotion of caring has been cultivated within him enough so that he makes a stand on the islander's behalf. After he wins, the elder will then tell him that he has displayed true growth as a character, and that others are more needing of his caring and integrity. He'll then set off to rejoin the team.