Nami's log pose begins to point to the sky, after that, a big ship falls from sky and the crew finds a map in 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 doesn't 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.
Following a fight in the bar, Luffy, Zoro and Nami meet a man outside the bar who tells them that Sky Island does exist. As they leave Mock Town, they get into a fight with Masira's brother Shōjo, another salvage monkey.
The Straw Hats meet with Montblanc 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 outcasted 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 Shōjo 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're greeted by Conis and her pet, Suu. 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."
Before they can leave Chopper, Robin, Nami and Zorro are abducted by a giant shrimp. Luffy, Sanji and Usoppe go after them to the upper yard
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.
Satori is defeated by Luffy and Sanji. Mainwhile has Gan Fall been defeated and Chopper jumps in the water to rescue him.
Chopper is saved by a bunch of giant Southbirds, who tell him that Gan Fall was actually God. Nami, Zoro and Robin discover the reason why Upper Yard is a soil island: It was once part of Jaya, and this is the part that Liar Norland saw. Meanwhile the Shandians attack Upper Yard.
The Shandians' attack on Upper Yard has started. The crew is finally reunited, and everyone speaks up about what has happened. Chopper takes care of Gan Fall, and the pirates plan to steal the gold on the island.
After befriending a wolf pack, Gan Fall tells the crew a little more about the history of Upper Yard.
Eneru takes away the limitations of the priests. Also, Usopp witnesses a mysterious person fixing the ship; the next day Merry is found to be back to her original form. After getting her off the altar, the pirates plan out their course of action.
A giant python makes Luffy, Robin, Chopper and Zoro split while going to the ruins at the south.
Wyper takes out Shura and tells his goal to the Shandians, and Eneru speaks up about how many people will be alive by the end of his plan.
Zoro fights the Shandian warrior Braham, and defeats him with One Sword Style: 36 Caliber Phoenix technique.
Luffy fights Wyper, but after some time, he falls into some underground ruins. Meanwhile, Eneru appears on the Going Merry and after telling that his true goal was the City of Gold, he takes out both Usopp and Sanji; then he vanishes and leaves Satori's brothers: Hotori and Kotori to avenge him.
Chopper is attacked by Gedatsu, who turns out to be a complete moron, and eventually defeats him, sending him plummeting to the Blue Sea. Conis and Pagaya help Aisa, and head to Upper Yard.
Eneru defeats several members of the Shandian Tribe. Meanwhile, Gan Fall and Nami start and finish their fight with Kotori and Hotori. Hotori is defeated by Nami while Kotori is defeated by Gan Fall.
While Robin is looking at some ruins she found, Yama, The Chief Enforcer, attacks her. Yama is easily defeated by Robin. Later, she discovers the legendary city, Shandora.
Priest Ohm appears and starts fighting everyone.
At the Upper Ruins, the fight between Ohm, Zoro, Gan Fall and Wyper begins. When Nami appears, she is swallowed by the giant python, along with Gan Fall and Aisa.
Ohm makes matters worse, creating a barbed wire cage around the area. Laki is knocked out by Eneru, and Nami, Aisa, and Gan Fall find out why the python was rampaging so much.
Zoro finally defeats Priest Ohm with his 108 Caliber Phoenix technique. Meanwhile Pagaya and Conis hear the terrible truth about the goal of Eneru: to eradicate every person in the sky.
Eneru appears only to reduce the group as close to his prediction as he can.
Eneru counterattacks Gan Fall and lands a finishing hit. He then knocks out Robin as she tries to manipulate him. Zoro impresses Eneru with his power but is easily beaten, while trying to make him pay for what he did to Robin; but it takes Wyper with a secret weapon to take Eneru down.
Eneru defeats Zoro and Wyper. Upon seeing this, Nami follows him to a cave where his ark, Maxim, is. Luffy finally gets out of the snake, along with Aisa, only to find out the outcome of the fight against Eneru. When Aisa tells him that she knows where he is, he asks her to take him there.
Luffy and Eneru start fighting. Conis tells the dangers of staying in Sky Island to the other Skypieans.
Eneru starts a machine that would bring the death of Sky Island: Deathpiea.
Luffy falls from the ark. Nami starts fighting Eneru while Sanji and Usopp try to rescue her.
Usopp and Sanji split up to rescue Nami, but the first one to get on deck is Usopp.
Eneru's thunderclouds are coming down to Sky Island while the evacuation is half complete.
The history of Norland and Calgara is told, as a flashback from Wyper.
Norland and Calgara are enjoying themselves, as well as the villagers and Norland's crew, but that changes one day, as the villagers start hating their new friends.
The cause of the hatred is discovered and explained. Meanwhile, Calgara vows to meet Norland again.
Angel Island is destroyed by Eneru's attacks. Luffy decides to go and ring the golden bell before Eneru takes it away.
Nami finds out a way to get to Eneru, by cutting down Giant Jack. Wyper finds out from Robin that Norland has a descendant that is searching for the Gold City, and that's the reason why Luffy wants to ring the Golden Bell.
Luffy defeats Eneru, ringing the Golden Bell in the process.
The 400 year war on Sky Island comes to an end. Montblanc Cricket and the Masira Brothers hear the Golden Bell ringing and realize that the Gold City was always in the sky. Eneru, who was thrown to the Blue Sea heads out to the Fairy Vearth (the Moon). The Sky People (both Skypieans and shandians) celebrate the end of the war with a great bonfire.
Robin deciphers the poneglyphs on the Golden Bell and realizes how to find the Rio Poneglyph. She also discovers poneglyphs on the Bell that were written by Gol D. Roger, who could understand poneglyphs, who had discovered the Rio Poneglyph, and had once visited Skypiea. Soon afterwards, the Straw Hats steal a bunch of gold from the Giant Anaconda's belly and they begin to leave Skypiea.
The Golden Bell rings as the Straw Hats are going down to the sea, meaning that they are welcome and are deeply thankful for what they did. When the ship finally rests on the sea, problems appear, as the ship has landed in a Marine base.