After a number of events Crono's party experiences, including acquiring the broken pieces (hilt and blade) of the sword as well as the red mineral (Dreamstone) from which it's made, Melchior repairs the Masamune sword. Crono then takes it to Frog who joins his party. They travel to the Magic Cave and, using the Masamune's power, Frog opens up the rock wall so they can enter the Cave which leads to Magus's Lair.
While battling Magus in his Lair, Frog uses the Masamune to weaken him.
When Crono's party finds Cyrus' tombstone in the Northern Ruins in 600 A.D., Frog pays his respects. Knowing Frog is safe, Cyrus' spirit is released and able to move on to the afterlife. But before he goes, he energizes the Masamune making it more powerful. That's when Masa and Mune appear for a moment, eager to see the new blade in action.