This page explains how to complete the Cyrus's Ghost sidequest in Chrono Trigger.
Start the Quest
Put Frog in the lead of your party and, in 600 A.D., find a previously unreachable little continent called Choras. It's east and south of Ozzie's Fort.
Go to the Cafe and talk to the drinking guy, who laments about his stolen tools. Now, go to Choras, 1000 A.D. and visit the Choras Inn. Talk to the drinking guy, who asks you to get the tools from his wife. So go to "Residence" and talk to his wife.
With tools in hand, head back to the drinking guy in 600 A.D. and give him his tools. Follow him to his house, and converse. Then head to the Northern Ruins. He'll tell you there are monsters preventing him from completing the repairs.
With Frog, Lucca, and possibly Magus in tow, first head left. Fight the Sentries on the way (Fire is good, Shadow is bad), then continue right. Beat these Sentries the same way, but leave the chest alone. This is the same deal as those upgrading-type chests in Guardia castle: they get better with age.
Instead, go back the way you came, fight the Sentries, and go up and continue to the right of the entrance. Go through the door.
There are several paths here, all of them containing monsters. So just go left, up, and right in turn, and beat the monsters with magic.
When that's all done, leave the ruins and talk to the builder. Pay, then return to the ruins, but this time without Magus.
Now you can take the left path all the way to the end, where Cyrus's grave awaits. With Frog in your party, check the tombstone to start a scene. When it's over, the original Masamune is powered up. Equip it now, and the Hero Medal. You won't need to change Frog's weapon for the rest of the game.
Now go back to that builder and pay him yet again, then head for the Northern Ruins once more.
Take the right path. DON'T OPEN ANY CHESTS! If you see a magical sealed chest, check on it, but don't open it. There are monsters in the north path, including Bases that have a powerful Slash attack. Heal up if they Slash you. Red Pin works very well against them.
When you are done, go out to Epoch and go to 1000 A.D.
Back in the ruins, reap the rewards of your 400 year long "wait". There is a Magic Tab to the left of Cyrus's Grave in 1000 A.D., and a Power Tab in the bottom left corner of the first room you reach when you take the path to the right. Then, go back to 600 A.D. and open the chests to get the original items.
Also, if you have Frog in the lead and you go to the place in the Denadoro Mountains where the Free Lancer is throwing stones, Frog will catch the stone and you get the Gold Rock. This opens triple tech Grand Dream.