After the Going Merry narrowly escapes being hit by a "sea train", the crew meets an old woman, Kokoro, and her granddaughter, Chimney. Kokoro gives Luffy a map to Water Seven. Luffy, Nami, and Usopp buy boats driven by sea monsters called "yagara".

Luffy, Nami, and Usopp get strange greetings from the residents and they get to experience the roller coaster-like channels of Water Seven. Luffy find out that some pirates had been beaten at the hands of some powerful craftsmen; the Galley La Company. Chopper loses Robin and some strange new people threaten Zoro back on the ship.

The people who attacked Zoro reveal themselves to be the feared "Franky Family", though they're no match for Zoro. Luffy have their gold exchanged for cash. After, they meet a man who resembles Usopp, Galley La's carpenter employment foreman, Kaku. Usopp's cut of the money is stolen by the Franky Family.

Paulie makes his debut when he retrieves Usopp's stolen money as he runs from debt collectors. Kalifa shows Luffy, Nami, and Usopp around Dock No. 1 and tells them how Iceburg founded the Galley La Company. Kaku returns from the Going Merry and tells them that their keel is irreparably damaged.

Luffy refuses to believe that Galley La cannot repair the Going Merry. The two soon realize that not only is Usopp missing now, but the two brief cases that were returned to them are empty. Nami decides to head to Franky House and finds Usopp on the way in a pitiful state. As she heads back to the ship for help, Usopp goes to the Franky House himself.

Luffy, Sanji, Zoro, and Chopper follow Usopp's bloody trail to the Franky House, where they find him passed out in front. The four of them challenge the Franky Family only to find out that their real target, Franky himself, is gone and has taken the money with him.

Once they're back on the ship, Luffy has to finally tell Usopp that the Going Merry can no longer be repaired and that they've chosen to get a new ship without him. Usopp believes that Luffy has abandoned the dignity of their ship and says he's leaving the crew. That night, he challenges Luffy to a duel.

Usopp fights Luffy in order to decide who keeps the Going Merry; he fights harder than he's ever fought before. Luffy actually seems to pose no threat but all the while, he's remembering what great friends they used to be, sailing together on the same ship. Even after taking a harsh beating, Luffy defeats Usopp. They leave Usopp and the ship behind.

The Strawhats get themselves a hotel room. Nami finds the crew on the roof with urgent news: Iceburg has been shot. As the Galley La Company frantically search for answers, Nami and Luffy decide to check on his condition – only to be met by closed gates. Franky appears then to exact his revenge – with style.

In the streets outside of the hospital, Luffy fights Franky. Inside, Iceburg recalls seeing Nico Robin and another tall man before he was shot. The Galley La company run outside and stop Franky and Luffy and tell them that they suspect the Strawhat Pirates of the crime.

The Galley La Company continues to fight Luffy and Franky is enraged that they've stolen his opponent. An incredibly high tide called the "Aqua Laguna" is coming and Chopper and Sanji rush to warn Usopp. Luffy raises some chaos in order to meet with Iceburg and he demands to know what's happening. Iceburg says he wants to see Robin one more time.

In a bar, Franky talks with Kokoro about her theory on who shot Iceburg. The rumors she speaks of seem to have some truth as we see Robin meeting with someone from an organization called CP9. While the crew hide from angry residents, Sanji and Chopper discover Robin and she tells them what they've feared: she's responsible and she wants to part ways.

Chopper reunites with the others without Sanji and they discuss what's happened. Luffy decides that in order to know the full truth, they must catch Robin. Usopp attempts to repair the ship enough to withstand the Aqua Laguna and the Strawhats make their way to the Galley La Company.

The Strawhats (still missing Sanji) rush to Galley La where Robin and CP9 begin a raid. In Iceburg's room, Robin and the mysterious man Iceburg saw before, tell him that they've purposely placed the blame on the pirates. Their true aim is the blueprints he would've passed down to Paulie. Luffy separates from his group.

Robin speaks with Iceburg inside his room still. We already know that Robin can read the poneglyphs - and it seems Iceburg is the one with the blueprints to the ultimate weapon, Pluton. The true enemies are revealed to be Iceburg's own allies. Elsewhere, Luffy is tied up with Paulie after Paulie tells members of CP9 that his blueprints are fake.

Lucci tells Iceburg their hypothesis and has Kaku check his pulse to tell if the things he tells him are true. They suspect that Iceburg's friend from the past, Cutty Flam, is really Franky and it's revealed to be true. Therefore, Franky has the real blueprints. The Strawhat Pirates and Paulie break into the room where they find Iceburg and CP9.

Luffy and the others request that Robin comes back to the crew. She refuses and tells them that she cannot accomplish her "wish" if she were to stay with them. Robin turns to leave and CP9 try to hold the pirates back. Robin successfully escapes and Lucci shows those remaining his "transformation".

Lucci's transformation is a result of a Devil's Fruit; a Zoan Type leopard. He quickly disposes of the crew and CP9 tie up Paulie and Iceburg, leaving them alone as the building slowly burns down around them. In Franky's underground hideout, Usopp tells him his story and Franky is finally touched. In return, Franky tells him a little about Tom's contributions to Water Seven.

Usopp believes that the person who repaired the Going Merry in Skypeia was really the Going Merry itself. Franky says that the ship was inhabited by a spirit who enters ships who are dearly cared for. The spirit repaired their ship just enough for them to reach the next island. The doorbell rings from the sea side and the Galley La foremen enter.

The foremen discover Franky's hidden room and he fears they'll trample his memories. A long flashback ensues, covering Franky's past in Tom's Workers and how he and Iceburg helped create the Sea Train.

Spandam, a CP5 representative, was determined to get Tom proven guilty in his trial so he could get the blueprints. As Franky walked into the town, people from the government began to attack with the battleships he had personally constructed. Tom and Iceburg run to their shipyard where they're attacked by two ships which also destroy the others. Iceburg tells Franky that he has to take responsibility or he'll never forgive him.

Franky said that if a ship of his were to be used as a weapon, then it's no longer one of his ships. That enraged Tom and he punched Franky for the first time, telling him he had to take pride in the ships he created. He then told the judge that he would accept the punishment for both his previous crime and the recent attack. Franky tried to stop the train to Enies Lobby with his bare hands.

Chopper escapes the burning building with Paulie and Iceburg on his back and collapses outside. Iceburg tells Nami that CP9 threatened to destroy the Straw Hats if Robin didn't cooperate with them. Nami rushes to tell Chopper so they can go looking for the rest of the crew. Elsewhere, the foremen let go of the Going Merry so she would be destroyed at sea.

Paulie helps clear the name of the Strawhats but doesn't tell the mob everything he knows. He gets the mob to follow Chopper so they can search for the rest of the crew. Nami goes her own way so she can rush to the Sea Train. As Nami nears the station, Sanji, ahead of her, approaches the train

Nami and the conductors are rescued by Paulie when the Aqua Laguna floods the main station. A man hands Nami a letter he found from Sanji. It informs her that Usopp, Franky, and he are on board the train that had just departed. On board, he storms the cars. High up in the city, Nami speaks with Kokoro and spots Luffy, stuck in between two buildings, in the back streets where the Aqua Laguna will hit first.

Nami finally reaches Luffy and tells him that he needs to hurry before Robin reaches Enies Lobby. Chopper finds Zoro and hands him the Sandai Kitetsu so he can escape the chimney. Luffy pushes apart the buildings he was stuck between and Paulie grabs them all so they can escape the Aqua Laguna's massive wave.

Sanji fights his way through another train car and finds Usopp and Franky. Seeing how determined Luffy is to save Robin, Kokoro and Iceburg lends the Strawhat crew the use of another sea train, Rocket Man. The Franky Family shows up, pleading with Luffy to let them join them because they'll do anything for their leader.

The Rocket Man finally makes it out to sea. As the train connects with the tracks, Luffy has to rescue Chimney before she's thrown off by the wind. In the meanwhile, Iceburg has a flashback about when he finally met Franky again in Water Seven. With Luffy and Chimney safe in the train, Paulie tells his fellow carpenters who the real culprits were. The Strawhats, Franky Family, and Galley La Company form an alliance.

Luffy and Zoro perform a move that acts similar to a cannon and blasts a hole through the wall of the tidal wave ahead of them, opening up a channel for them to pass through. They miraculously pass through unscathed and the passengers rejoice. Sanji contacts the rest of the crew and fills them in on his current situation. Usopp separates from them but later, when Sanji and Franky are spotted, a man named Sogeking comes to their rescue.

Sogeking makes his grand entrance. Franky and Sanji aren't fooled by his costume but they try to humor him. They devise a plan first, then detach the last two cars and fight their way through the rest. Back in the Rocket Man, Luffy, Zoro, Nami, and Chopper get an outfit change; Nami shows off the weapon Usopp upgraded for her while he was still with them.

Franky's fight with Nero continues. Nero discovers that Franky's weak spot is his back, so Franky lies down flat so he can't get to it. Nero demands that he fight seriously, so Franky gets up to perform his "Centaur" form. Sogeking talks with Robin and tells her that the crew knows about her reasons for leaving. Those on the Rocket Man encounter the discarded cars and Zoro slices them so they can pass.

Zoro clashes with "Ship Cutter" T-Bone. The fight is short and Zoro joins the crew again in the Rocket Man. On the Puffing Tom, Sanji beats Wanze beautiful, though Wanze thinks he's ruined his face. Franky finally gains the upper hand against Nero and defeats him. After beating their respective opponents, Franky and Sanji stand to fight against the other CP9.

After hiding under Robin's cloak for a few episodes, Sogeking finally shows himself. They stumble into the room with the CP9 and meet with Sanji and Franky. Sogeking produces a smokescreen. The four head into another car, detach it, and escape. It's not long before Blueno pulls their car back, though. Franky knocks down the wall so they can escape but ends up on the enemy car. Blueno opens a door then back in the Strawhat car.

Robin willingly follows Blueno into his improvised door and Sogeking and Sanji are left alone. For a while, Blueno explains a little of Robin's past involving the Buster Call. Back at the Rocket Man, Yokuzuna the frog jumps onto the front of the train, knocking them from the rails. After Kokoro speaks with him, he joins the group. The CP9, Franky, and Robin finally reach Enies Lobby and disembark.