So, when you go to the new boss, the profit is there, and he was talk about how they beat lavos and something powerful is up ahead, so he goes into the portal, so you go into the portal, and it shows Magus fighting it. Keep in mind, you can have Magus in the party as well. (i haven't check to see if magus says to this other magus.) So after Magus looses, the party fights the new final boss, even though you "win" the battle, the monster isn't dead and the party gets knocked out, then the other magus comes back, and talks to Schala, she sends the party back to there time, and then magus and schala talk, then he leaves.. then another scene with magus talking about his effort in searching for her, after that's over, a forest scene appears, and magus walks out from some trees, only to have lost his memory...
and that's it.