forthwith I shall slay Magus and restore honor!
While I'm not sure if you need Frog for this, I had him in my party so I'm going to include it. Time to start for the Rainbow Shell! Go to 600 AD, to C village's cafe and talk to Toma. He'll give you some pop to pour on his grave if he doesn't make it back. Return to 1000 AD and go to the West Cape grave and pour the pop on the grave. Toma will appear and tell the group where he found the Rainbow Shell. He will then fully pass on. (Rest of this quest is finished by going to the area shown and dealing with Marle's family problems.)
Go to the mansion to the north and when inside go to the left. There is this knight ghost. Fight him and nothing you do will hurt him, so just keep it to psychical attacks. He will realize who he is attacking and stop, he will then disappear. Now go back to the cafe that you got the pop from Toma and there is a man drinking at the table, he has lost his tools! Go to 1000 AD and talk to a man that looks like him in the cafe and he'll let you borrow his tools. Take them back to 600 AD and talk to the man, then go tot he residence and he'll fix up the mansion to the north. Go there and the group is told that they cannot continue until the monsters gone. They leave and you can explore a bit more. Go back to the left and down the stairs and up to the grave that's there.
It's Cyrus's grave and there isn't really a nice message on it. Frog will talk to Cyrus a little. (If you have Magus in the party he will cover himself with his cloak.) Frog realizes a few things here and tells Cyrus that he has been avenged. The Masamune is now upgraded and is the best weapon for Frog once again.
After that is done, you can go back and talk to the carpenter at his house and you'll have to pay him but he'll fix the mansion. It happens a couple of times but you can get some good weapons and armor. When you click on the boxes tell it no, go back 1000 AD to open the boxes the previous items will morph into the better ones and then you can go pick up the other items in 600 AD.