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.

Paulie helps clear the name of the Straw Hats but does not 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.

Chopper escapes the burning building with Paulie and Iceburg on his back and collapses outside. Iceburg makes it clear to Nami that Robin wanted to recover the blueprints and to do that, she wanted her companions to leave the island without her. 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.

(Franky's flashback) 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.

(Franky's flashback) 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 are attacked by two ships which also destroy the others. Iceburg tells Franky that he has to take responsibility or he will never forgive him.

CP9 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.

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 CP9 enter.

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 7.

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 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 Straw Hat Pirates and Paulie break into the room where they find Iceburg and CP9.

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.

The Straw Hats (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.

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 Straw Hats make their way to the Galley La Company.

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.

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 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 Straw Hat Pirates of the crime.

The Straw Hats 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.

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.

Once they are 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.

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.

Luffy refuses to believe that Galley La cannot repair the Going Merry. The two soon realize that not only is Usopp missing now, 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.

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.

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

Luffy, Nami, and Usopp get strange greetings from the residents and they get to experience the roller coaster-like channels of Water 7. Luffy's group finds 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.

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 7.

Luffy insists on fighting Aokiji alone and risks it all so the crew can save the frozen Robin. 

The man they met, Marine High Admiral Aokiji, appears to be incredibly lazy. He first displays his Devil's Fruit ability by freezing the sea so some deserted people can get off the island. Unfortunately, he's determined to catch Robin. Luffy, Sanji, and Zoro attack but they seem to be no match.

Once Foxy wins back his crew, he captures the Straw Hats. Nami and Luffy fight Foxy and although he's defeated, his crew accepts him back. Later, they sail to an island where they meet someone Robin knows: a Marine named Aokiji.

Luffy rescues Foxy, Hamburg, and Porche from a storm at sea. When they reunite with the Sexy Foxy ship, they find it captained by somebody new. Foxy accepts a Davy Back Fight in order to regain his ship and crew. Donning the afro once again, Luffy vows to defeat the captain.

Luffy returns and knocks some sense into Zoro. Cornered, the sea horse spreads illusions of the people in their memories to distract them. It steals their complete memories and claims that it has become a Sennenryu. Luffy defeats it and returns all the memories but the townspeople are convinced they are the memory stealers.

On their way to "The Palace of the Sea God" Robin's group meets an entranced Zoro. It looks like Zoro wants to fight so Luffy urges the others to keep going without him. They apprehend the kid but the whistle was what was really stealing their memories. Zoro returns, still entranced, but Luffy's nowhere to be seen.

During the night, Usopp, Chopper, and Sanji question what brought them to the Going Merry. In the morning, Usopp builds them a raft and they sail to the island where they meet Nami again. Meanwhile, the boy sets his sights on Zoro.

Robin suggests that only those who were sleeping lost their memories. Luffy and the others then remember seeing the mysterious boy who played some kind of flute. Later that night, they discover the boy outside and Luffy tries to fight him. At the last second, he proclaims his memory has returned.

A mysterious figure appears during the night and steals the memories of the crew. In the morning, Robin is the only one who remembers the Straw Hats adventures together. Her attempts to keep the crew together fail as Nami and Zoro go separate ways.

Luffy manages to finally defeat Foxy by using his ability against him. After dismissing his new crewmembers, the Straw Hats leave in search for a shipwright.

Luffy continues to battle Foxy with the odds not in his favor, and the fight continues inside Foxy's ship.

With Chopper gone again from Luffy's crew, Luffy and Foxy face off in the final game: a battle of brawn aboard Foxy's ship.

Foxy decides to take Robin from Luffy this time because of her Devil Fruit ability. The next match is a race to the top of the island.

With Luffy's victory, he takes Chopper back, but foolishly accepts another challenge by Foxy.