The film opens on Vice-Admiral Monkey D. Garp and Fleet Admiral Sengoku being warned by Shiki using his Devil Fruit powers to destroy the marine vessels. On a floating island, Monkey D. Luffy is chased by a genetically-enhanced animal. The monster is overcome by another, which in turn battles another several times until Luffy finally defeats the fourth monster.
The Straw Hats have been separated into three groups: Sanji with Usopp, Roronoa Zoro with Tony Tony Chopper, and Nico Robin with Franky and Brook.
Shiki reveals that Nami has been taken to this place against her will and a brief flashback is shown: several days earlier, the Straw Hats read news of an attack on East Blue. Luffy vows to protect the East Blue before witnessing Shiki's ship overhead. After escaping a storm, Shiki meets Nami and reveals his powers to make any inanimate object he touches float. After learning it was Nami that delivered the warning, Shiki offers to take them there before escaping with Nami. The others try to rescue her, but Shiki makes the pirates scatter on the island
Shiki asks Nami to become his navigator but she refuses. Dr. Indigo appears with an 'evolved' bird, called Billy, that can use electricity, demonstrating it to Shiki, but after being electrocuted by it, Shiki rejects it. He reveals that a plant, called IQ, can cause animals to evolve instantly and to increase strength along the way. Nami protects Billy, and the bird is left with her as Shiki and his men leave. Meanwhile, Sanji and Usopp battle various animals while Sanji searches for Robin and Nami. Meanwhile, Zoro and Chopper rescue a young girl, Xiao, and are lead to her village and are told about the large poisonous plants around the village. However, long term exposure to the plants is poisonous to humans, and the girl's grandmother has become ill by it. Xiao was looking for the cure which is the IQ plant, but Shiki has stolen the IQ plants for his experiments. Sanji and Usopp learn that Shiki also takes all the men and young women to his royal palace, leaving the village with only the very young and old, before meeting up with Zoro and Chopper
Nami manages to escape her captivity with the help of Billy, and finds the Thousand Sunny along with Luffy. Shiki's plan soon becomes apparent. Robin's group discovers that he is planning to release the animals on the island into East Blue to force the World Government's surrender and that he is planning a demonstration against a village on the floating island to show their power.
The two join the others at the village, and they also learn of the plan from the village residents. Shiki, in an attempt to capture her, confronts and defeats the Straw Hats. Nami is forced to rejoin Shiki at the cost of her village. Nami records a message, using the tone dial, which is supposed to be a farewell message. Robin's group arrives shortly after and rejoin the rest of the crew. Xiao gives the pirates a tone dial and they hear Nami's message, to Luffy's anger
Nami attempts to destroy the plants protecting his palace, but gets poisoned herself. Shiki traps her near the plants and heads off to meet the pirate captains gathering. While greeting them, the Straw Hats burst into the palace and engages Shiki and his henchmen. The group manages to defeat them while Chopper and Usopp are ordered to search for Nami. Nami is found by Billy who helps destroy the plants just as Usopp and Chopper arrive. Chopper soon realizes the only way to save Nami is to find the IQ medicine, but Shiki attempts to stop them. Luffy engages Shiki in a duel. The two find the IQ plant, but find the medicine is being held by Dr. Indigo. Zoro manages to defeat Dr. Indigo and Nami recovers. Sanji and Brook, meanwhile, witness another of Shiki's henchmen, Scarlet, attempting to kiss Robin. Sanji manages to defeats Scarlet
Shiki brutally injures Luffy when he receives a storm warning from his Transponder Snail, asking him to redirect the island. The call was in fact coerced by Usopp and Chopper, and that Nami has lead them directly into the storm. Upon realizing this, the remaining pirates retreat, while the Straw Hats rig the palace with explosives. Shiki refocuses his attention on the Straw Hats, but Luffy uses an electric charge and knocks Shiki to the ground, leaving Luffy victorious.
Nami attempts to destroy the plants protecting his palace, but gets poisoned herself. Shiki traps her near the plants and heads off to meet the pirate captains gathering. While greeting them, the Straw Hats burst into the palace and engages Shiki and his henchmen. The group manages to defeat them while Chopper and Usopp are ordered to search for Nami. Nami is found by Billy who helps destroy the plants just as Usopp and Chopper arrive. Chopper soon realizes the only way to save Nami is to find the IQ medicine, but Shiki attempts to stop them. Luffy engages Shiki in a duel. The two find the IQ plant, but find the medicine is being held by Dr. Indigo. Zoro manages to defeat Dr. Indigo and Nami recovers. Sanji and Brook, meanwhile, witness another of Shiki's henchmen, Scarlet, attempting to kiss Robin. Sanji manages to defeats Scarlet
Shiki brutally injures Luffy when he receives a storm warning from his Transponder Snail, asking him to redirect the island. The call was in fact coerced by Usopp and Chopper, and that Nami has lead them directly into the storm. Upon realizing this, the remaining pirates retreat, while the Straw Hats rig the palace with explosives. Shiki refocuses his attention on the Straw Hats, but Luffy uses an electric charge and knocks Shiki to the ground, leaving Luffy victorious.
The other Straw Hats escape with the Thousand Sunny, using Shiki's pirate sail as a parachute. Luffy is recovered by Billy while the villagers are shown flying away using the wings on their arms. The Marines capture the retreating pirates, including Shiki. As the Marines witness the islands crash into the sea, now free of Shiki's power, they spot the Thousand Sunny. However, the Straw Hats manage to escape. At the end of the film, Luffy learns that Nami's message had ended with the crew being asked to save her