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CONTAINS SPOILERS
Firing an arrow into the distance through a stone arch
Jefferson's clue: "Since the Frog King flooded the lands to the east, many old structures have become inaccessible. One such structure can still be reached..." Take the Flooded Fortress door and go northwest near the entrance until you see a stone arch floating in the water. Shoot an arrow through it to activate the switch on the other side. A path will be created to reach the secret.