Exclusive to the GameCube re-release is a set of unlockable bonus content colloquially referred to by fans as "The Three Secrets". The requirements for earning this content is as follows:
•All discoveries need to be found and reported
•The number of opened Treasure Chests must be at 90% or above
•All Crew Members must be acquired
•All Moonfish need to be captured and given to Maria's bird Piccolo
•All Wanted Battle bounties must be found, beaten, and reported
•Beat all four optional battles with Piastol and finish her story
•Defeat over 2500 enemies
•Defeat all four Sky beasts
•Win 12 non-story Ship Battles

Upon meeting this criteria, The Three Secrets can then be acquired:
1. The Mystery Merchant will now sell the Sky Fang sword to Vyse.
2. A secret discovery can be found on a peak of a rocky overpass in High Sky just outside of Sailor's Island. This discovery is a Golden Hamachou, and does not appear in the Journal after it is found.
3. At Crescent Isle, a hidden boss Spoiler:Vigoro, who in the GameCube version became an Air Pirate following his third encounter with the main characters can be fought.