With the help of Toma, Crono's party finds the Rainbow Shell in the Giant's Claw in 600 A.D. Since it's too heavy to carry out, they recruit Guardia soldiers to help transport it back to Guardia Castle, where it's stored away as a national treasure.
In 1000 A.D., the Chancellor, who is actually Yakra XIII in disguise, uses the Rainbow Shell in his plot to overthrow King Guardia XXXIII and take over the Kingdom. He accuses the King of selling it for his own personal gain. But Crono's party finds it hidden away in the Castle, so they come back with proof that it's still there. Later, Melchior uses the Rainbow Shell, combined with the Sun Stone, to create stronger weapons for Crono's party.