On a floating island, Shiki Naoto Takenaka uses his Devil Fruit powers to destroy marine ships and warn Monkey D. Garp Hiroshi Naka and Fleet Admiral Sengoku Takkô Ishimori. The Straw Hats are scattered into three groups: Sanji Hiroaki Hirata and Usopp Kappei Yamaguchi; Zoro Kazuya Nakai and Chopper Ikue Otani; and Robin Yuriko Yamaguchi, Franky Kazuki Yao, and Brook Cho.
Meanwhile, Nami Akemi Okamura is on the island with Shiki, who reveals his power to float himself and anything he touches. After learning she delivered the warning, Shiki offers to take them there before abducting Nami. The others attempt a rescue, but Shiki scatters the pirates and strengthens his hold. He tries to recruit Nami as his navigator, but she refuses. His minion Dr. Indigo Ryusei Nakao demonstrates an evolved bird named Billy Yasuhiro Takato who can generate electricity, though Shiki soon discards it after Dr. Indigo is electrocuted. He also explains that a plant called IQ can make animals evolve instantly and gain extraordinary strength along the way.
Nami protects Billy, leaving the bird in her care. Sanji and Usopp clash with various beasts while Sanji searches for Robin and Nami. Simultaneously, Zoro Kazuya Nakai and Chopper Ikue Otani save a young girl named Xiao Wasabi Mizuta, who leads them to her village and warns them about large poisonous plants that threaten the people. She explains that the cure lies with the IQ plant, which Shiki has stolen for his experiments. Sanji and Usopp learn that Shiki has taken all the men and young women to his royal palace, leaving the village populated mostly by the very young and the very old. The party reunites with Zoro and Chopper, and Nami flees with Billy, eventually discovering the Thousand Sunny.
Robin's group, led by Nico Robin Yuriko Yamaguchi, learns that Shiki plans to unleash the island’s animals on East Blue to force the World Government’s surrender and to mount a show of power against a village on the floating island. They join the others at the village and uncover Shiki’s plan. Shiki confronts the crew and defeats several of them, offering Nami a place beside him if the Cocoyashi Village will be spared. Robin's team arrives and rejoins the Straw Hats. Xiao hands them a tone dial, and they replay what appears to be Nami’s farewell message, though Luffy Mayumi Tanaka erupts in anger and storms off.
Nami tries to destroy the protective plants around Shiki’s palace but is poisoned in the process. Shiki traps her near the plants and heads to meet a gathering of pirate captains. The Straw Hats launch a preemptive strike against Shiki and his henchmen. The group defeats them while Chopper and Usopp search for Nami. Billy finds Nami and helps them destroy the plants just as Usopp and Chopper arrive. Chopper grasps that the only way to save Nami is to obtain the IQ medicine, but Shiki stands in the way. Luffy Mayumi Tanaka engages Shiki in a duel, and the two find the IQ plant, but the medicine is held by Dr. Indigo. Zoro Kazuya Nakai defeats Dr. Indigo, and Nami recovers. Sanji Hiroaki Hirata and Brook Cho witness Captain Scarlet Banjo Ginga attempting to kiss Robin, and Sanji defeats Scarlet. Nami, Usopp, and Chopper trick Shiki into steering his ship toward the island, forcing his crew to flee. The Straw Hats rig the palace with explosives.
Shiki refocuses on the Straw Hats, but Luffy uses an electric charge created by Usopp to knock Shiki to the ground, leaving Luffy victorious. The others escape with the Thousand Sunny, using Shiki’s pirate sail as a parachute, while Luffy is rescued by Billy as villagers fly away on wings sprouting from their arms. The Marines capture the retreating pirates, including Shiki, as the islands crash into the sea and the Thousand Sunny comes into view. Luffy learns that Nami’s message was really an SOS, asking the crew to save her, and he tries to listen to the end while Nami, embarrassed, grabs the tone dial and lets it slip out of reach.
