After departing Water 7, the Straw Hats find a drifting ship with hungry and sick fishermen. All things seem great until the drifting fishermen have something else in mind and set a trap for the Straw Hats.
The Straw Hats find themselves surrounded by a fleet of Marine ships, actually illusions. They escape using the Soldier Dock System, with the fishermen in tow. Chopper meanwhile is told by Jiro about their past of being the Phoenix Pirates under Puzzle. The Accino family meanwhile pledges to collect the Straw Hats' heads.
Trapped by moving icebergs, the Straw Hats try to figure a way out avoiding numerous dangers as the assassins draw closer. The Phoenix Pirate, Puzzle, awakes after Chopper's treatment only to reveal some harsh realities on the awaiting crew. The Thousand Sunny is trapped by ice by three of the assassins. However it escapes using the Coup de Burst. Zoro, as usual, is lost after severing a blocking iceberg in half, and in an iceberg attack the rope attached to the Phoenix Pirate ship is severed leaving behind Luffy and Chopper. Their pirate flag is then stolen by a little girl's flying fish.
Using the Shark Submarine, Nami and Franky find out that penguins are moving the icebergs. Afterwards, they are attacked by Hockera. Usopp and Sanji are knocked off the Sunny by an iceberg, and encounter Sarco and Albelle. Luffy and Chopper, along with the rest of the Phoenix Pirates are attacked by Blindo, and Lil, the little girl, appears before Robin back on the Sunny. Finally, Zoro stumbles upon Lovely Land, the Accino Family's HQ. The fight between the Accino Family and the Straw Hats begin.
The fights continue. Luffy, distracted due to the lost flag, has initial trouble with Blindo, but the Phoenix Pirates help capture him. Usopp has marginal success against Albelle, but is hampered by the angered Sarco. Franky, meanwhile, manages to beat Hockera at the cost of his remaining cola, but ends up iced up inside the sub along with Nami. Lil accepts Robin's request to be led to Lovely Land, where Zoro is aimlessly wandering inside it.
Due to more of Sanji's blundering, he and Usopp find themselves captured by Sarco and Albelle. Meanwhile, Canpacino arrives at the Phoenix Pirates' ship to rescue his brother. Due to their 'brotherly love', the two are human magnets, and use their unique fighting style to separate Luffy from the others. Zoro, meanwhile, encounters the Don. After knocking back a few drinks together, the Straw Hats' jolly roger is delivered, and Zoro's 120 million bounty is quite a hard thing to pass up...
The Don reveals the power of the Heat Heat Fruit: the power to melt any substance. Zoro is no match against his anger and ends up imprisoned inside an ice cavern along with the other captured Straw Hats. They manage to escape thanks to some indirect assistance from Robin, who is still with Lil. Luffy's fight with Blindo and Canpacino ends in a draw when the two leave to calm down the Don. Puzzle finally overcomes his depression and resolves to follow Luffy, Chopper, and Jiro to Lovely Land to recover the pirate flags.
The formerly captured Staw Hats finally manage to get outside, no thanks to Zoro, where they once again encounter the Accinos. The rematches turn out to be in the Straw Hats' favor, as Hockera is taken down by Franky and Chopper, Albelle and Sarco by Nami and Sanji, and after a protracted battle, Luffy smashes Blindo right back into Lovely Land. Puzzle, showing newfound confidence, then confronts Canpacino. But all the ruckus arouses the Don. Meanwhile, Robin is taken hostage by Lil to coerce her into promising to stay in Lovely Land.
The Heat Heat Fruit gives the Don all sorts of powers, from throwing blasts of heat, heating his skin to extreme temperatures, to even being able to fly by blowing steam out his nose. How can Luffy win when he can barely even hit his enemy? Meanwhile, Puzzle defeats Canpacino, the rest of the Straw Hats search for their flag, and Robin and Lil reconcile with one another. Outside, the fight really heats up when Luffy activates Gear Second, but the Don isn't going to fall so easily.
After a grueling struggle, Luffy finally defeats the Don with a red-hot Bazooka. With a little help from Lil, the two stolen flags are finally recovered, and the crew manages to get it back on the ship before Luffy returns. The defeated Accinos sail away with the Don in tow and finally have a belated birthday celebration, while Albelle makes up with her sister. The Phoenix Pirates go to battle with Canpaccino and the remaining grunts, Puzzle promising to meet the Straw Hats again in the New World.
Chopperman and Namifia are low on money! Dr. Usodabada constructs a plan to bring down Chopperman while collecting fame for himself and a new crew to replace his nonhelpful duo—Sanjilops and Zorogilla. His plan—to take over the TV Station and televise his demands. Not that anyone really cares except Chopperman, who only wants to join for the rare Air Force C-Max Collectors item. After a wrestling match between the two, and even a mecha battle, the evil Doctor is defeated, and Chopperman reaches celebrity status!
In search of food, the Straw Hats attempt octopus hunting before discovering a barrel in the middle of the ocean. After opening the barrel, Thousand Sunny gets thrown into the foggy Florian Triangle where it encounters a ruined ship and a skeleton man named Brook, whom Luffy immediately asks to join the crew.
Onboard the Thousand Sunny, Brook tells his story of being a musician before being killed. However, his spirit was able to reanimate his skeleton due to the power of the Revive Revive Fruit. He also tells of having his shadow stolen, and thus cannot be out in open sunlight. A ghost suddenly appears in the galley, and the Straw Hats find out that they have been targeted by the ghost isle Thriller Bark, which has found them.
Brook bids farewell to the Straw Hats and leaps overboard, revealing that he can dash across the ocean's surface. Nami, Usopp, and Chopper sail out to explore the island using the Mini-Merry II, and encounter a cerberus. Back on the ship, the remaining crew members are harassed by an invisible creature. After fleeing the cerberus, Nami, Usopp, and Chopper encounter Hildon, a vampiric creature who offers to take them to the mansion of Doctor Hogback.
Usopp, Nami and Chopper traverse through the forest of Thriller Bark, where they are attacked by a platoon of zombies before finally reaching the mansion of the bizarre surgeon Doctor Hogback and his female assistant Victoria Cindry. While immediately hospitable, the doctor starts acting strange after it is mentioned that Brook has arrived on the island. The Thousand Sunny, meanwhile, gets caught in a giant spiderweb.
After the meeting with Hogback, Nami is assaulted by an invisible creature in the shower, but Usopp and Chopper manage to drive it off. The rest of the Straw Hats set foot on the island and encounter more zombies. Elsewhere, Hogback meets with Absalom, the invisible man who attacked Nami, and a ghost referred to as Perona, to discuss what to do with the Straw Hats. Back in the manor, Nami, Usopp, and Chopper find themselves surrounded and trapped by the Surprise Zombies: zombies that strike from paintings, taxidermied heads, and even floor rugs.
Escaping from the Surprise Zombies of the mansion, Nami, Chopper and Usopp discover the truth about Victoria Cindry's true identity and Doctor Hogback's experiments before being approached by a mysterious samurai zombie with Brook's voice. Meanwhile, Luffy's group are ambushed by ghosts who make them become depressed but then depart. They destroy a platoon of outside zombies with a group team attack.
After beating the zombies, the Straw Hats learn that one of the Shichibukai, Gecko Moria, has been stealing people's shadows and using them to revive zombies. After they leave, Absalom rallies the zombies together for the Night Attack, while the ghosts from before return to their master, a Gothic Lolita-style Ghost Princess Perona. Gecko Moria himself, a massive, giant-like man, is awoken. The Straw Hats come to the realization that Thriller Bark is not an island, but rather, a massive ship!
Usopp, Nami and Chopper are effortlessly incapacitated by the General Zombie Ryuuma, a samurai with an eerie resemblance to Brook, and are locked inside a coffin. Luffy and the others enter the mansion and defeat the Surprise Zombies with ease, but Sanji goes missing, so they force Buhichuck to act as their guide by taking him with them. While the zombies of Thriller Bark celebrate the start of the Night Attack, Absalom awakens the other General Zombies to handle the Straw Hats.
Luffy, Zoro, Robin, and Franky head forward in an attempt to find and rescue their missing nakama. Meanwhile, Nami, Chopper, and Usopp are transported toward the main part of the mansion, but are accidentally detoured and find themselves in Perona's Wonder Garden!
As Luffy, Franky, and Robin face a closed room of powerful Armored Zombies, Nami, Chopper, and Usopp are protected by the dog-zombie Inuppe, who resembles Sanji in behavior!
With Luffy captured next, Franky and Robin face the Armored Zombies and the Zombie General Talaran! Elsewhere, Lola attacks Nami out of jealousy.
Robin, Franky, and Brook take on the Zombie General Talaran, as Nami, Usopp, and Chopper defend against Lola. Elsewhere, Luffy encounters Moria!
After finishing off General Talaran, Brook reveals the mysteries behind Thriller Bark. Elsewhere, Moria gathers the Mysterious Three and attempts to capture Luffy's shadow.
Moria and the others begin the revival of number 900 - Oz. Meanwhile, Franky and Robin learn more of Brook's past and their future mission.
As Oz awakens, Nami, Usopp, and Chopper are discovered! Can they flee and reach the Sunny in time, or will Absalom capture them first?
After Oz eats his full, will he obey Moria? Elsewhere, as Brook prepares to fight Ryuuma a second time, he recalls his first encounter with him five years earlier.
Usopp and the others return to the Sunny in search of Luffy, Zoro, and Sanji. When they arrive, they discover the trio unconscious. After waking them up, Usopp and Franky each share what they have discovered. But, Franky has a shocking story about Brook's promise to his nakama. Meanwhile, Nami's wedding with Absalom draws near.
After learning that Brook's nakama is Laboon the whale, Luffy is dead-set on recruiting him. Before they prepare to take down Thriller Bark and regain their shadows, Sanji tells Chopper, Robin, and Franky the story of Laboon and the Twin Capes.
With their goals in mind, Luffy, Sanji, Robin, Usopp, and Chopper go after Nami and Moria! Meanwhile, Franky and Zoro head toward Brook. However, Hildon tells the others of the Straw Hat's plan.
Luffy continues on to take on Moria while Chopper and Robin remain behind to take on Hogback and his loyal zombie servants. After Oars runs off with a new pirate hat from his destruction, the remainder of the crew end up in Perona's room where she uses her negative powers on them. However, Usopp reveals that he's immune to her attacks because he's already got a negative personality, staying behind to take on the ghost princess while the others continue towards Absalom and Ryuuma.
Usopp continues to stand up to Perona's Negative Hollows while wiping out Wild Zombies, while Brook is held at the mercy of Ryuma, who finally proves his superiority over the original by defeating the skeleton in battle before the arrival of Zoro. Meanwhile, Oars continues to cause chaos on Thriller Bark, forcing Absalom to send his entire General Zombie audience to stop him. But Oars annihilates all of them with a "non-Gum-Gum" Gatling, leaving their boss at the mercy of the newly arriving Sanji.
Luffy attempts to attack Gecko Moria, but instead is forced to face his shadow clone: Doppelman, while Usopp continues to maneuver around the Wild Zombies to get to Perona only to now face Bearsy's wrath. Sanji saves Nami from Absalom, who doesn't see him as a threat due to the power of his zombie, but Sanji unleashes his own rage against the lion-faced man, both for harming the women of the crew as well as an unknown connection between the two of them.
It looked like the end for Sanji as Absalom used his devil fruit ability, but Sanji comes back with his anger and starts beating Absalom to death, after revealing he always desired the See-through See-through Fruit the devil fruit which allowed Absalom to turn invisible. Meanwhile Luffy is still having trouble with Gecko Moria's Shadow the Doppleman who uses him to turn into bats, Luffy finally finds a way to attack Moria by using Gum Gum Stamp! The Hollow Hollow fruit user, Perona, is still being chased by Usopp who in turn is being chased by Bearsy, but Perona gets away. Usopp stops Bearsy and catches up to Perona who is floating in mid air out the window, she then calls herself the "Ghost Princess".
Usopp is forced to go through a gauntlet of Perona's Horo-Horo powers, including an untouchable body, size manipulation, passing right through him and creating mini-Hollows that slowly rip away at his stamina and body. Temporarily turning into Sogeking to finally remove Bearsy's shadow, Usopp is forced up against a desperate wall until he finally discovers Perona's weakness: her own room, where her real body lies helplessly while using her abilities!
The battle between Usopp and Perona continues; Usopp fires something at Perona's real body which seems to miss it, giving Perona the confidence to fight back again. This time she produces a huge hollow, at least four times the size of Usopp, which grabs Usopp in its mouth and won't let go, leaving Perona time to go and return to her body. She detonates it, but the explosion gets sucked into the impact Dial, which Usopp cleverly brought out. He uses this on a Zombie-Hippo which was sneaking up, breaking his arm, but he then reveals that he stuck Perona's arm to the wall; he wins the battle by firing hundreds of little moving fake cockroaches onto her, and then smacking her over the head with an inflatable ten-ton hammer.
Zoro duels Ryuma in Hogback's lab, while Franky guards over the injured Brook. Neither Zoro, nor Ryuma, can gain any advantage over the other, as they keep matching the other's attack. Their attacks quickly destroy the lab, forcing them to escape the room and continue their fierce duel on the roof. As Brook watches on, he comes the conclusion that Ryuma was never taking their fights seriously. After an intense sword fight, during which the entire roof collapses to the ground below, Zoro finally defeats Ryuma using a technique which sets him ablaze. Zoro lands hard on the lip of the roof below. Ryuma manages to land on a higher ledge. Ryuma staggers slightly, then acknowledges his defeat at Zoro's hands. Sheathing Shunsui, Ryuma throws it to Zoro. Ryuma collapses in a bout of flames and Brook's shadow is finally returned to him, to his great joy. Zoro acknowledges Ryuma's skill as a swordsman and says he wishes he could have met Ryuuma before he died. He also agrees to forget the outcome of their fight.
Chopper and Robin are outmatched by Zoro and Sanji's zombies, both of whom have almost completely lost the personalities they acquired from their shadows. Chopper tells Hogback that he had once respected him, but does not anymore after realizing the true nature of Hogbacks experiments. Hogback, however, argues that the zombies are truly alive, and recalls that he had fallen in love with Cindry while she was alive, only to have her reject him in favor of her fiancé. After her death, Hogback agreed to serve Moria in exchange for reviving her. Chopper becomes furious and attempts to attack and purify Cindry, but Cindry's strength, and Zoro and Sanji's zombies prevent them from doing so. Zoro's zombie and Sanji's zombie begin fighting each other, still unable to get along, and Robin tricks Hogback into telling them to jump out of the tower. Hogback orders Cindry to attack, but Cindry, having temporarily regained her original self, is unable to move. Elsewhere, Luffy is still unable to hit Moria, and Oars arrives at their location.
Oars appears declaring his submission to Moria. Moria instructs him to hunt down the Straw hat pirates. Oars attacks Luffy. Luffy escapes and starts chasing Moria who flees the scene. Hogback without Cindry's support tries to run away. Chopper catches him and is helped by Robin against him. The fight is interrupted by Oars' attack smashing through the ceiling. Sanji, distracted by all this, lets his guard down letting Absalom take Nami away. Everyone runs out of the mansion and Oars calls out for the Straw hat crew to come forth and face him.
Oars begins fighting Sanji, Zoro, Franky, Brook, Robin, Usopp and Chopper, having inherited Luffy's fighting style but lost his memories. The crew tries to fight against him, but learns that he is incredibly strong and fast, even if he is unable to stretch like Luffy can. Oars manages to apparently knock out all seven of his opponents. Elsewhere, Absalom attempts to resume his wedding to Nami, and Luffy continues pursuing Moria, as the chase leads him into the forest.
Perona finally wakes up and is brought up to date with the current events on Thriller Bark. She decides to run away. Nami also wakes up to see that she is in a wedding ceremony with Absalom. Lola interrupts the wedding giving Nami a chance to escape. Absalom brings Lola down. Nami takes revenge by beating Absalom. Luffy continues chasing Moria and Oars who is looking for the rest of the Straw hats. But everyone who he thought he had defeated is back up on their feet ready for a second round.
The Straw Hats attempt a "docking" maneuver by hanging onto Franky in order to form a "Giant Robot Warrior", but it fails when Robin refuses to participate, as she considers it too embarrassing. The Straw Hats combine their strengths to get Oars off-balance and cause him to fall to the ground, enraging him. Brook is absent from the battle, as he leaves to find milk to drink to heal his wounds. Elsewhere, Nami attempts to find the treasure of Thriller Bark, but discovers that it is empty. Perona's subordinates load the treasure and food onto the Thousand Sunny when they see the Shichibukai Bartholomew Kuma aboard, looking for Moria.
Taking advantage of several weaknesses, including his stupidity and similarities to Luffy, the Straw Hats continue to wear away at Oars, yet his continued persistence allows Zoro to test his new sword Shuusui for battle. Meanwhile, Kuma tries to find out Moria's location from Perona, yet her defiance forces him to make her disappear with an ungloved hand before speaking with Nami about his "choice to be here". Luffy appears to catch Moria again, only to discover it is Doppelman.
Moria's shadow escapes, leaving Luffy stranded in the forest, as some strange people reveal that they are looking for him. Zoro begins the fight against Oars, revealing the new 108 Caliber Phoenix with his newly-obtained sword, but Oars manages to avoid his attacks. Kuma informs Moria of the appointment of Blackbeard as Crocodile's replacement, and warns him that the Straw Hat pirates may defeat him, too. Moria refuses Kuma's offer to help him, and enters Oars' stomach to guide him against the crew. The crew realize that as Luffy failed to catch and defeat Moria, it is up to them to defeat Moria and Oars before dawn. Usopp runs to the kitchen to gather more salt to purify Oars, but Oars strikes out at him, destroying the passage to the kitchen. Brook, his injuries healed, manages to save Usopp and bring the Straw Hats a large bag of salt.
With Moria's guidance, Oars is better able to counter the Straw Hats' strategies and turn their attacks against them. Franky is knocked unconscious after a failed attempt to fire himself at Oars with a giant slingshot known as Kuwagata and shoot him at point-blank range with Weapons Left. Nami arrives and joins the battle, but Oars demonstrates that he can somehow stretch his limbs, which the crew realizes is Moria's doing. Elsewhere, Luffy meets up with the Rolling Pirates, whose shadows have been stolen by Moria. They plant shadows into him in order to multiply his fighting strength and grant him new skills so that he can defeat Moria.
Moria explains that he enabled Oars to stretch by stretching his shadow, thereby forcing his body to stretch along with it in order to ensure that the body and shadow are the same shape. Usopp fires Brook out of Kuwagata, with Robin making him spin and Nami electrifying him, but he only does minor damage to Oars and is knocked out when Oars retaliates. Robin attempts to use her powers on Moria, but he attacks her with his shadow and then switches places with it, rendering her attack useless. He then takes her shadow, rendering her unconscious. Chopper discovered that Oars died of frostbite, and that while he does not feel any pain, he can still take damage from their attacks. Sanji and Chopper launch a combo attack on Oars, who then knocks out both of them with Gum Gum Gatling, leaving only Nami, Zoro and Usopp standing.
Zoro tries attacking Oars' arm again, but Oars knocks him out by kneeing him into a wall. Usopp shoots Brook's salt into Oars' mouth with Kuwagata, but Moria's shadow catches it and throws it out, breaking the bag and preventing them from using it again. Oars tries to stomp Usopp and Nami, but Nightmare Luffy arrives and gets them to safety in an instant. While the Rolling Pirates take the unconscious Straw Hats to safety, Luffy begins attacking Oars, and with his shadows, is far stronger than his opponent. Moria attempts to escape, but Luffy punches him out with Gum Gum Pistol and sends Oars flying with Gum Gum Storm. The shadows leave Luffy's body, but he appears to have won.
Oars recovers from Nightmare Luffy's attack. However, the Strawhats all get back on their feet, from Luffy to Brook, and launch a final devastating attack on Oars, which ends with Luffy smashing a Gigant Bazooka into Oars' face from above, breaking his spine and finally defeating the demon. Moria, however, gets out of Oars' stomach moments later, and prepares himself for his ultimate technique, Shadows Asgard. By sucking up all of the shadows of all of the zombies on Thriller Bark, totaling one thousand shadows, Moria becomes a grotesque monster, as big as Oars in size with short spindly legs, gigantic arms, and a huge bloated neck pulsating with veins.
Luffy begins fighting Moria, entering Gear Second in the process, but the blows that he deals to Moria are not enough to force him to release the shadows. Moria attacks Luffy with a devastating blow, but he manages to continue fighting, and activates Gear Third while Gear Second is still active. With a new technique, Gum Gum Gigant Jet Shell, he knocks Moria under the collapsing mast of Thriller Bark and forces him to release all his shadows just as dawn arrives. However, the ones who had their shadows stolen start to vanish.
All of Moria's victims recover their shadow and celebrate regaining their ability to enter daylight. Luffy, Zoro, Sanji and Robin recover their shadows in time to avoid being disintegrated. Luffy lies unconscious from his wounds and using Gear Second against Moria, and Usopp worries about him endangering himself by having to use the technique on the stronger enemies ahead. Kuma receives orders from the World Government to kill everyone on Thriller Bark in order to cover up Moria's defeat. He attacks the survivors with a strange move that sends several people flying backwards, before turning his attention to Zoro.
Zoro attacks Kuma, who reveals that he has eaten the Paw-pad Paw-pad fruit, and shows his ability to repel attacks, move considerable distances almost instantly and repel the air to attack his opponents. Zoro is quickly outmatched, and Sanji and Usopp's attempts to help him are rendered futile by Kuma's hard body and ability to block projectiles. Kuma then offers to spare the survivors of Thriller Bark if they turn over Luffy, but they unanimously refuse. He then detonates a paw print full of compressed air, devastating the island.
While almost everyone on the island is knocked out in the blast, Zoro slashes Kuma with Shishi Sonson, but sees that it is ineffective, as Kuma is a Pacifista, a cyborg whose body is harder than steel. Seeing that he can no longer fight, Zoro offers his life to save Luffy, saying that he cannot hope to become the world's best swordsman if he cannot protect his captain. Sanji attempts to take Zoro's place, but Zoro knocks him out. As part of his agreement with Kuma, Zoro takes in all of Luffy's pain and fatigue, which Kuma says would kill him if he suffered it on top of his already severe wounds. Zoro takes in the pain, and Kuma leaves, remarking on how Luffy has a loyal crew. Luffy regains consciousness, surprisingly energetic, while Zoro emerges from his sacrifice near death.
Hogback and Absalom escape Thriller Bark with the unconscious Moria, and reveal that Blackbeard gained his status as a Shichibukai by defeating Ace. The next day, the Straw Hats celebrate their victory over Moria, but do not know why Zoro is so badly wounded. Sanji hears the story from the Risky Brothers, but prevents them from telling anyone else, saying it would trouble Luffy greatly to hear that Zoro suffered for his sake, but Robin eavesdrops on the conversation. Luffy tells Brook that Laboon is alive, and he is overjoyed to hear it, and begins to think about the time 50 years ago when he and his pirate crew first met Laboon.
Brook recalls his past, when the whale Laboon started following his pirate ship and befriended the crew. When the crew headed toward the Grand Line, they had no choice but to leave Laboon behind because the danger the sea would present to a young whale like him, but Laboon followed them over Reverse Mountain, anyway. Brook and his captain convince Laboon to stay behind, promising that after they traveled through the entire Grand Line and he grew strong enough to follow them, they would come back and bring him on their adventures. They were unable to fulfill the promise, though.
Brook recalls the Rumbar Pirates' journey through the Grand Line, where they faced many dangers but still managed to enjoy themselves. The captain contracted an illness and attempted to leave the Grand Line through the Calm Belt with the other infected crew, leaving Brook in charge of the remaining pirates. The journey continued until some powerful enemies defeated the Rumbar Pirates in the Florian Triangle, fatally poisoning them. As they were dying, they sang Binks's Booze one last time, recording it in a Tone Dial in the hopes that Brook would revive with his Devil Fruit power and deliver the shell to Laboon. Back in the present, Brook silently hopes Laboon will wait just a little longer for his return.
Brook tells Luffy that he is glad to be alive and asks if he can join the crew, which Luffy approves of. All the Straw Hats are shocked by this, except for Zoro, who is sleeping, and Robin, who knew Luffy would accept him no matter what, but they nevertheless welcome him to the crew. Two days later, Usopp and Franky make a grave for the dead Rumbar Pirates, and Zoro lays the broken Yubashiri at the grave. Nami gets a Vivre Card from Lola, which points the way to Lola's mother, a pirate in the New World. Luffy takes out the piece of paper he received from Ace, which is also a Vivre Card, and learns that as it is burning and shrinking, Ace's life is in danger. Believing that Ace can get out of trouble on his own, Luffy decides to head onward rather than go to rescue him, and the Straw Hats sail away from Thriller Bark. As the Luffy and his crew sail away, three enormous and mysterious figure appears in the fog, looking over Thriller Bark.