Exclusive to the GameCube re-release is a set of unlockable bonus content that is 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.