In search of food, the Straw Hats attempt octopus hunting before discovering a barrel in the middle of the ocean. After opening the barrel, with fireworks launched from it, the Thousand Sunny gets thrown into the foggy Florian Triangle where it encounters a ruined ship with a living skeleton on it. While the others are unnerved, Luffy boards the ship with Sanji and Nami where they find the skeleton. After the skeleton introduces himself as Brook, Luffy immediately asks him 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 the lightness of his body allows him to dash across the ocean's surface. Nami, Usopp, and Chopper sail out to explore the island using the Mini-Merry II, ending up getting knocked onto land before they are chased by a patchwork cerberus that is a third fox. 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, Chopper revealing Doctor Hogback to be a famous surgeon and expressing excitement to see him. But when the group have second thoughts of heading towards Hogback's manor, due to the strange creatures roaming the wood, Hildon is nowhere to be seen before being attacked by a platoon of zombies that drive them towards the direction of the manor. While immediately hospitable, despite the manners of his female assistant Victoria Cindry, Hogback 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, who frightens Chopper by insisting that no one is allowed in his laboratory, Nami takes a shower with Usopp and Chopper outside while musing her thoughts on their situation. But Nami finds herself restrained by an invisible man in the shower, the figure fleeing when Usopp and Chopper manage to drive him off. The invisible man meets with Hogback and the ghost, referred as Perona, to discuss what to do with the Straw Hats. As the rest of the crew set foot on Thriller Bark, Luffy taming the cerberus as the group encounter more zombie creatures, Nami, Usopp, and Chopper attempt to leave the manor. But the trio instead find themselves surrounded by the Surprise Zombies: zombies that strike from paintings, taxidermied heads, and even floor rugs.

While evading the Surprise Zombies upon finding a secret passage, Nami, Chopper and Usopp discover the truth about Victoria Cindry being a starlet who died long ago. They eventually found the door to Hogback's laboratory, observing the scientist from outside before they are found by a mysterious samurai zombie who sounds like Brook. Meanwhile, Luffy's group are ambushed by ghosts who briefly made them depressed before they reach the graveyard where they are ambushed by the zombies.

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 Ryuma and 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 Oinkchuck to act as their guide by taking him with them. While the zombies of Thriller Bark celebrate the start of the Night Raid, Absalom awakens the other General Zombies to handle the Straw Hats.

After awakening the General Zombies, Absalom is accosted by Lola, a zombie warhog obsessed with making him her husband. After learning that he's chosen Nami to be his bride, Lola sets her sights on the navigator. Nami, Usopp, and Chopper manage to escape their coffin and find themselves in a garden, surrounded by animal zombies, including a bizarre penguin-bulldog zombie named Inuppe who talks and acts a lot like Sanji. The other Straw Hats, meanwhile, discover a hallway lined with suits of armor, and realize that Zoro is now missing as well.

As Perona makes her way to the Thousand Sunny to get the Straw Hats' treasure while Absalom attempts to stop Lola from hunting Nami, who realizes Innupe's uncanniness to Sanji, Luffy, Robin, and Frankie are lured by Oinkchuck into a room where they are forced to face an army of armored General Zombies. Though they are able to handle them, the three Straw Hats decide that evading them is top priority. But while Frankie and Robin escaped, Luffy's route was blocked by a zombie swordsman named Jigoro who acts much like Zoro. Luffy is captured by the zombie forces, with Franky and Robin surrounded by both sides by the generals and a massive monkey-spider named Taralan.

Despite Absalom's attempts to halt Lola and abduct Nami to be her bride, both intents failed as the latter flees from Lola with Usopp and Chopper unable to slow the warthog zombie down. While the Wild Zombies disrespected his orders for them to not harm Nami, Absalom puts the lot in their place while venting his bad mode on Inuppe by blasting him into a wall for his insolence. At the same time, Franky and Robin buy some time against the Taralan and the General Zombies by the former destroying the bridge to trap the zombies in the courtyard while Robin flies them to the area of the castle behind Taralan. As Taralan was about to pursue them, Brook suddenly falls from the sky.

When Usopp and Chopper are unable to halt Lola, Nami manages to quell the warthog's bloodlust by claiming to be a male crossdresser while encouraging her to take more violent steps in getting Absalom's affections. But when Absalom manages to evade Lola, Nami, Usopp, and Chopper hide inside Perona's servant Kumacy who is unable to reveal the pirates' location as they overhear Absalom and Perona talking about being summoned by Moria as he obtained an ideal shadow for his ultimate Special Zombie: Luffy. Meanwhile, after their enemy used his webs to reach them, Franky gets the upper hand against Taralan until Robin is immobilized by the Spider Mice, the ones behind the abductions of Sanji and Zoro. Luckily, Brook jumped up to help the two pirates, promising to tell them the full story while easily defeating Taralan.

After defeating Taralan and releasing his shadow soul from within, Brook explains to Robin and Franky the truth that the zombies of Thriller Bark are actually corpses animated by shadows taken by Gecko Moria from his victims via the power of his Shadow-Shadow Fruit. Meanwhile, Moria meets with the rest of the Mysterious Four (as well as the hidden Straw Hats in Kumacy) where he uses his powers to steal Luffy's shadow to use his Special Zombie.

With Luffy's shadow, Moria and his followers head into the freezer holding his ultimate special zombie that he believes will help him gain power in the New World: the massive ancient warrior known as Oars. At the same time Brook parts ways from Franky and Robin after giving further crucial advice regarding the zombies, and answering Franky's request, so he can go forth to accomplish his own goal: defeating the zombie Ryuma and reclaiming his shadow from the samurai fencer.

With Usopp, Chopper and Nami bearing witness, Moria implants Luffy's shadow inside the corpse of Oars. Within moments, the massive zombie comes to life with three Straw Hats discovered by Moria's gang. Luckily, Oars immediately displaying aspects of Luffy's personality by yelling out for food, the three Straw Hat pirates escape in midst of the giant's revival. However, they do not get far as Nami is abducted by Absalom for the marriage he plans for her while Usopp and Chopper are left to fend for themselves against numerous platoons of zombies before being rescued by Franky and Robin.

Brook confronts Ryuma, recalling his time on Thriller Bark five years prior - and his first battle with Ryuma and how he lost to a zombie with his own shadow. Ryuma mocks Brook for being so careful about his afro, and the two engage in another battle. Oars meanwhile continues to exhibit Luffy's personality traits as he devours most of Thriller Bark's food while declaring his desire to be King of the Pirates.

Usopp, Chopper, Robin and Franky return to the Sunny, discovering their ship had been ransacked before waking up Luffy, Zoro and Sanji. After informing the three about their current status and Nami's abduction, Franky reveals that he asked Brook before they parted way of is what driving him as he could not really return to society due to his appearance. Brook reveals that he and his crew made a promise to return to Reverse Mountain where they left a valuable friend fifty years ago. Luffy, Zoro, Usopp and Sanji are astonished to find out that friend Brook referred to is the whale Laboon.

Luffy, Usopp, Sanji, and Zoro tell the rest of the crew how they got to meet Laboon as they started their new journey, while Brook reflects on his promise to return to Laboon amidst his duel with Ryuma. Luffy declares his intention to make Brook a part of their crew, and the Straw Hats prepare to counterattack the forces of Thriller Bark in order to reclaim what was stolen from them.

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 who sics Jigoro and Inuppe on them. After Oars runs off with a new pirate hat from his destruction, his actions disrupting Abalsom as his wedding to Nami is almost complete, the remainder of the crew end up in Perona's room where she uses her negative powers on them. But Usopp reveals that he's immune to her attacks due his negative personality, staying behind to take on the ghost princess while the others continue towards Absalom and Ryuuma.

As Usopp continues to stand up to Perona's Negative Hollows while wiping out Wild Zombies, Brook is greatly overpowered by Ryuma was about to defeat the skeleton when Zoro arrives. Meanwhile, Oars continues to cause chaos on Thriller Bark, forcing Absalom to send his entire General Zombie audience to stop him. But Abolsom learns that Oars annihilated all of the General Zombies with a "non-Gum-Gum" Gatling before Sanji arrives, Luffy having found Gecko Moria and expressing his intent to beat him up.

As Luffy finds himself facing Gecko Moria's animated shadow Doppelman while attempting to attack Moria, Usopp manages to dispatch the Wild Zombies and chases after a frighten Perona with Kumacy chasing after him. Though Absalom initially believed Sanji to not be a threat as he easily dispatched Inuppe, he is shocked that the pirate able to actual due harm to his heavily modified body. Having placed Nami's unconscious body on a pew, Sanji explains that he has more of a beef with Absalom besides his actions against the women in his crew.

Beating Absalom when he refused to reveal he has been using firearms, Sanji reveals that he knows Absalom's invisibility is due to the Clear-Clear Fruit which he wanted for his own reasons. As Sanji defeats Abalsom, Luffy managed to get through Doppleman to land a hit on Gecko Moria with his Gum Gum Stamp. At the same time, losing sight of Perona, Usopp finally manages to give Kumacy the slip before finding a more confident Perona floating in mid air out the window.

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 explosive mini-Hollows that slowly rip away at his stamina and body. Temporarily turning into Sniperking to finally dispatch Kumacy, Usopp is forced up against a desperate wall until he finally realizes Perona's sudden change. Usopp uses one of his attacks to destroy a nearby wall, revealing Perona's body lying helplessly in her bedroom.

Having deduced that Perona used her Horo-Horo powers to project her spirit, Usopp attempts to fire an attack at it. But the attack appeared to miss with Perona producing a Special Hollow bomb to hold Usopp while she returned to her body. Usopp luckily uses an Impact Dial to absorb the explosive force, using it to take out the Wild Zombie Hippo Gentleman with some injury as consequence. Usopp then reveals that he actually fired an adhesive on Perona's body, beating her by scaring the trapped girl to death with toy cockroaches and an inflatable ten-ton hammer. As Chopper begins to notice Jigoro and Inuppe acting less like Zoro and Sanji, Oars undergoes the same transition and makes his way back to Gecko Moriah. Meanwhile, Zoro and Ryuma's fight is getting intense as Brook tells Franky that Ryuma is actually fighting for real.