Crono's party heads to the West Cape in 1000 A.D. where they use the pop they got from Toma in Choras in 600 A.D. and pour it on Toma's grave stone. Toma's ghost appears and directs them to the Giant's Claw in 600 A.D.
The party then heads to the Giant's Claw, battling prehistoric creatures, and finally reach the Rainbow Shell. The Shell is so massive it's too difficult the carry out, so they head to Guardia Castle to get help from King Guardia XXI. The King sends soldiers out to the Giant's Claw to bring the Rainbow Shell back to the Castle, locking it away as a national treasure.
The party returns to Guardia Castle in 1000 A.D. to find that King Guardia XXXIII, Marle's father, is on trial for allegedly selling the Rainbow Shell for his own personal gain. The party searches the Castle for the store room and find the Rainbow Shell hidden away. They also discover that there is a plot by the Chancellor to overthrow the King and take over the Kingdom of Guardia.
Bringing back a shard of the Rainbow Shell as proof, Marle crashes through the stained-glass window of the Courtroom to save her father. The Chancellor then reveals himself to be Yakra XIII, the descendant of Yakra bent on revenge.
Yakra XIII is defeated and the bond between Marle and the King is mended. They also rescue the real Chancellor from a locked treasure chest. Melchior then shows up at the Castle and uses the Rainbow Shell, combined with the Sun Stone, to create more powerful weapons and accessories for Crono's party.