Game NotesAttack Magus with the same elemental that he uses. If you can't, do physical attacks to change his barrier. Have Frog attack with the Masamune to lower his defense and start pounding him!
The fight with Magus is the longest Boss fight up until this point in the game. To start with, he will perform various elemental magic. After any particular spell, his weakness will be the same as the Element he used. If you don't have access to that Element, hit him with a Physical attack to make him cast a new spell and change his barrier. Note that Frog's Masamune is an exception—this won't cause him to counterattack, and will actually lower his defense.
Eventually Magus drops his elemental defense and just starts hitting you with powerful spells. Now is the time for an all-out assault!.