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 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.

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.