Catch when thrown at you by the bird in Denadoro Mountains, 600 AD. In vanilla, you would need to have the upgraded Masamune equipped with Frog at the head of the party. In Jets these requirements don't exist; you can catch the rock with any party at any time.
In Giant's Claw, 600 AD, at the very end of the cave room that begins at the upper right and ends at the lower right (describe this better). Look north from the exit door that's along the south wall to see the treasure chest.
Laruba Ruins, 65,000,000 BC. Speak with the Nu at the north end. He will offer to change your lead character's name (you'll need to exit this dialogue first) and then give you a rock.
The hidden room in Kajar in Zeal. Open the books in order (water summons wind, wind makes fire dance) to open the secret room. Pick up the Poyozo doll to receive the rock.
Near the end of the Black Omen, the chest on the left side of the room where Terra Mutant is fought. Not available until you defeat the boss.