Beat the game then complete the following tasks to unlock the corresponding flag.
Unlock Arlong's Pirate Flag:
Defeat Arlong a second time around
Unlock Black Cat Pirate Flag:
Defeat kuro the second time around
Unlock Buggy's Pirate Flag:
Defeat Buggy the second time around
Unlock Kreig's Armada:
Defeat Don Kreig the second time around
Unlock Navy Flag:
Defeat Axe Hand Morgan or Chaser the second time around
Unlock Cook Pirate Flag:
Get Sanji and talk to Chef Zeff in 4-1
Unlock Alvida Pirate Flag:
Defeat Alvida in 1-1 then find her in 6-1
Unlock Veggie Pirate Flag:
It's located behind the Veggie Pirates in 3-1 (you need Ussop to get past them).
Unlock Straw Hat Pirates Flag:
Collect ALL the flags but the red hair pirates flag
Unlock Red Hair Pirates Flag:
Beat boss battle mode in ALL difficulties
Unlockables
Complete the following tasks to unlock the corresponding item.
Unlock Wado:
Complete level 1-2
Unlock Zolo's Stomach Band:
Complete level 1-3
Unlock Axe-hand Morgan Statue:
Complete level 1-3
Unlock Chouchou's dogfood:
Complete level 2-2
Unlock Map of the grand line:
Complete level 2-3
Unlock Special Buggy Ball:
Complete level 2-3
Unlock Chakram:
Complete level 3-2
Unlock Cat's Claw:
Complete level 3-3
Unlock Usopp's Sling shot:
Complete level 3-3
Unlock Mackerel Head One:
Complete level 4-1
Unlock Free Food:
Complete level 4-2
Unlock Gas Mask:
Complete level 4-3
Unlock Lollipop:
Complete level 4-3
Unlock Hatchan's Octopus Trap:
Complete level 5-2
Unlock Master of the Near Sea:
Complete level 5-2
Unlock Tooth Gum:
Complete level 5-3
Unlock Elephant Tuna On level 6-1:
Have Sanji talk to a woman
Unlock Shigure:
Complete level 6-2
Unlock Billow-A-Bike:
Complete level 6-3
Unlockable Modes
Unlock Boss Battle Mode:
Collect ALL the Coins
Unlock Mini-Game Mode:
Successfully complete the game once
