A group of pirates lead by Alvida plunder a ship, only to find a barrel which contains a strange boy named Luffy. Luffy is on a mission to find the legendary treasure "One Piece" and he befriends the ship's cabin-boy, Coby, who actually wants to become a marine officer. Luffy defeats Alvida and the two journey on in search of crewmates.

Luffy and Coby arrive at Shell Island, a Marine base. They meet the bounty hunter Roronoa Zoro, held under arrest by the infamous marine, Captain Morgan, and his son Helmeppo.

Luffy convinces Zoro to join his crew, but they must first defeat Captain Morgan. After freeing the island from Morgan's oppressive rule, Coby is accepted as a marine while the other two continue on their journey.

Navy Captain Koby comes to the Island of Women to arrest Pirate Empress Hancock with the new Pacifistas. While the Navy and Kuja fighters clash, Blackbeard comes to raid, also targeting Hancock.

Perona breaks into the Blackbeard Pirates' prison to rescue her captain, Gecko Moria, and frees Koby, who then helps free other prisoners. Koby, now with a high bounty, distracts a mob of pirates to protect the others. He recalls Blackbeard's plan to trade him for Hachinosu's entry into the World Government. The pirates face attacks from clay golems, SWORD member Kujaku, and a Marine force led by Garp and Tashigi.

A massive warship comes flying towards the Pirate Island of Beehive and Vice Admiral Garp launches a crushing attack on top of it to save his pupil Koby. Koby almost reaches the ship with Navy HQ Commander Hibari running by his side.

Kuzan, a former Navy Admiral, stands in the way of Garp who came to rescue Koby. He was once Garp’s pupil but is now a member of the Blackbeard Pirates. What happened to him after he was defeated by Sakazuki is now revealed.