Skull Rock is the 25th discovery that Vyse can make.
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“I never believed that old story about the skull pointing the way to hidden treasure. But one night, we was passing by it, and Moonlight from the full Moon reflected off Skull Rock and lit up an island in the distance…” - An anonymous sailor
It can be found on the Valuan continent, eastern side. If you've found the Balloon Flower, you can travel directly south from there to find it.
As implied by various sources in the game that lead the player to the discovery, if one aligns their ship precisely in the direction the skull is facing and travels straight until they hit land, they will arrive at Daccat's isle.