After their adventures in Alabasta, the crew come upon another deserted island and split up tasks amongst themselves. Chopper is left in charge of guarding the ship, and he reminisces about the day he first made the rumble ball and his first patient, Dr. Kureha, while spending some time with the newest crewmember: Nico Robin.

A weird salesman is fished out of the water and onto the Going Merry, and Nami buys a ton of "1000 year paper" from him to draw her sea maps. However, that's not going to be easy with the rest of the crew goofing off as usual.

The Going Merry runs into several Marine ships in some fog, and the Straw Hats meet a trainee Marine chef named Tajiyo. Sanji helps him out of a bit of cooking trouble.

The crew stops on an island that's having its annual fireworks festival; Usopp meets a young fireworks-maker named Kodama and helps her achieve her dream.

Zoro has a flashback about the time when he first met Johnny and Yosaku, and faced off against Bandits and, Dick.

After escaping from several Marine ships, the Straw Hats land on an uncharted island and meet an old man named Zenny. Chopper finds out that, because of his bad heart, Zenny probably only has three days to live.

The Straw Hats help Zenny out, hoping to make his last days good ones; they learn about Zenny's past as a money lender, and his dream of becoming a pirate. But Zoro realizes that Zenny has outlived Chopper's predictions and so the straw hats decide that, after helping him finish his pirate ship, they will leave the island.

Zenny decides to follow his dream and become a pirate, despite his age. He helps the Straw Hats out of trouble with the Marines, and then they part ways.

On Ruluka Island, some of the Straw Hats make enemies of the Mayor and his men, who have placed high taxes on everything. Robin, Usopp, and Luffy meet Professor Henzo, who's doing research on the island's rainbow mist. When some of the mist shows up, Henzo borrows the Going Merry to go explore it.

The inside of the Rainbow Mist full of wrecked ships and treasure, and is guarded by five kids. The kids are actually friends of Henzo's that got lost in the mist over 50 years ago.

Henzo, his friends, and the others try to find a way out of the ship graveyard. Meanwhile, the Mayor and his men let the information about the Rainbow Mist slip to the remaining Straw Hats still on Ruluka.

Luffy accidentally propels himself and Rapanui to the end of the mist. Nami appears in the ship graveyard with a rowboat full of treasure and a string connected to the real world, which are both stolen by Wetton's subordinate. The Mayor uses the Rainbow Tower to make a bridge to the Rainbow Mist.

The Going Merry escapes from the Rainbow Mist, getting badly damaged on the way. The Mayor gets arrested by a bunch of powerful marines that turn out to be older versions of Henzo's friends, who were thrown 50 years into the past by the Rainbow Mist's collapse.

Nami's log pose begins to point to the sky, and the crew finds a map of an island named 'Skypiea' on a 200-year-old ship. They compete with the monkey-like Masira's salvage crew while they search for more clues on how to get there.

The Straw Hats decide to go to Jaya island to look for information on Skypeia. Meanwhile, Ace suddenly shows up on Buggy's ship; Buggy does not let any of his men attack Ace, fearing Whitebeard's retribution.

Jaya's main town is full of famous pirates that are constantly brawling with each other. Luffy and Zoro have a run-in with a pirate known as 'Bellamy the Hyena,' who ridicules their dreams and beats them up.

Luffy, Zoro and Nami meet the man who is later revealed to be Blackbeard. They leave Mock Town, and get into a fight with Masira's brother Shoujou, another salvage monkey.

The Straw Hats meet with Mont Blanc Cricket on another part of Jaya; Cricket is a descendant of Montblanc Noland, an infamous "liar" who told of a gold city on Jaya, and Cricket was outcast for looking for artifacts of the gold city. He may be the only person who knows how to get to Skypiea.

Cricket explains how the Straw Hats can ride a dangerous vertical current called the Knock-Up Stream to get to Skypeia. However, they first have to catch a southbird to point them toward the point where the stream will erupt from the ocean.

While the Straw Hats are looking for a Southbird, Bellamy and his crew attack Cricket's house, and steal the gold artifacts he'd collected over the years from his salvage work. When the Straw Hats return and see what happened, Luffy decides to take a side trip back to Mock Town.

Luffy takes out Bellamy with a single punch. Meanwhile, the world government heads are concerned over Whitebeard, Shanks, and Luffy. The marines try to decide who will replace Crocodile as a Shichibukai - one of Blackbeard's crew shows up uninvited and nominates his captain.

The Going Merry is refitted by Masira and Shoujou to be more flight capable, and the Straw Hats catch a ride on the Knock-Up Stream for Skypeia.

The Straw Hats arrive in an ocean above the clouds. Usopp almost falls out of the Going Merry but is saved at the last minute. The crew is also attacked by a mysterious looking warrior, but is saved by the Knight of the Sky. Finally, they arrive at the border which transports them to the upper realm, Skypiea.

As the crew arrives in Skypiea, they are greeted by Conis and her pet Su. Both she and her father start explaining how the life in Skypiea is and how the different Dials work.

Nami finds out what should happen to anyone who enters the forest. Meanwhile, the rest of the gang are waiting for the wind to change but are rudely assaulted by Skypiea's police who are going to carry out Heaven's Judgement.

The Straw Hats have some problems with the local justice enforcer force called "The White Berets."

While trying to escape from Sky Island, Robin, Chopper, Nami and Zoro are held hostages by God Enel.

Conis leads Luffy, Usopp, and Sanji to a boat to get to Upper Yard, but she tells them it is a trap and almost gets hit by "Heaven's Judgment".

Luffy, Usopp and Sanji finally enter Upper Yard, only to find out that the whole road is trapped heavily, but at last they arrive at the Ordeal Gates. Meanwhile Robin, Zoro, and Nami go out to explore Upper Yard while Chopper stays behind to guard the ship.

Luffy, Sanji, and Usopp enter the Ordeal of Balls gate and encounter the Priest Satori.

Usopp, Sanji and Luffy fight Satori, but the power of Mantra seems to be too strong.

Chopper, threatened by priest Shura, blows the whistle for Gan Fall to come, but before he can arrive, Priest Shura assaults Chopper and begins destroying the Going Merry.