The film opens with a man singing “Ocean Guide”. “Black Arm” Zephyr (黒腕のゼファー, Kokuwan no Zefā), a former naval admiral and leader of the Neo Marines which also includes his henchmen Ain (アイン) and Binz (ビンズ, Binzu), commences an assault on the navy on Firs Island, a volcanic island and one of the End Points. While there, Zephyr steals the Dyna Stones and fights Kizaru and the marines before he starts an eruption to defeat the Admiral only to be sent flying into the ocean. While having a cherry blossom party, the Straw Hat Pirates discover an unconscious Zephyr floating on the sea. Luffy uses his gum gum devil fruit ability to reel him in, but when grabbing Zephyr’s prosthetic arm (the battle smasher) Luffy loses all his strength. The Straw hats soon learn that Zephyr’s arm is made with sea prism stones. As Chopper begins to attend to Zephyr’s wounds, Nami begins to worry, not just because of the prosthetic arm, but also because of Zephyr’s muscular form and his many battle scars, but Luffy reassures Nami that if Zephyr is a threat he will deal with him. When Zephyr comes too, everything is fine at first as Luffy and Zephyr begin socialising, but when Zephyr learns that Monkey D. Luffy is a pirate, he fights Luffy, Roronoa Zoro and Sanji. Having discovered Zephyr’s location with a Vivre Card, Ain and Binz join the ex-Admiral to fight them. Ain uses her Devil Fruit powers to de-age Nami, Tony Tony Chopper, Brook and Nico Robin, while Binz uses his Devil Fruit powers to trap Franky, Usopp and Brook with vines. Luffy goes one on one against Zephyr, but is overpowered and defeated when Zephyr grabs Luffy with his Battle Smasher arm. Realising that Luffy is the grandson of Monkey D. Garp, Zephyr attempts to kill them, but the Straw Hats are forced to flee. At Marine Headquarters, the navy discovers Zephyr’s whereabouts and decide to recover the Dyna Stones.
Landing on Dock Island, Franky repairs the Thousand Sunny, which has been damaged by Zephyr. They meet Mobston (モブストン, Mobusuton), whose granddaughter reveals that pirates who come to this island say that they have been attacked by Zephyr. Mobston, angered by Zephyr destroying their pirates’ dreams, decides to give the Straw Hats his strongest equipment. While there, the Straw Hats gather information on Zephyr’s location from the navy and meet up with Kuzan, who reveals that has left the navy after being defeated by Akainu on Punk Hazard. Using the Sea Train, the Straw Hats enter Secon Island just as the volcano erupts. They confront Zephyr, Ain and Binz, only to be easily defeated once again. Meanwhile, Garp reveals to Coby and Helmeppo that Zephyr once believed in the navy’s justice and became an Admiral after serving as a soldier in the navy. When Zephyr’s wife and son were killed by a pirate who resented him, Zephyr became an instructor. One day, most of Zephyr’s recruits were killed and Zephyr lost his arm after being attacked by a pirate with Devil Fruit powers. Zephyr acquired his prosthetic arm the Battle Smasher, a weapon developed by the navy’s scientist to defeat Devil Fruit users and organized a strike unit. However, when the pirate who attacked him was chosen to serve as a Warlord, Zephyr left the Navy, organizing the Neo Marines as a result.
Back on Dock Island, Kuzan reveals that Zephyr is targeting the three volcanic islands known as End Points. If all three islands erupt in a short period of time of each other, it would result in a giant eruption covering the world’s oceans and killing everyone in them. The Straw Hats confront the Neo Marines on the third End Point and have a massive battle. Luffy finds Zephyr and challenges him one to one. As the Straw Hats battle against the Neo Marines and a bunch of converted Pacifista’s, Zoro and Sanji go head to head against Ain and Binz. The Straw Hats are victorious, and with Ain defeated, Nami, Chopper, Robin and Brook return to their original age. Luffy and Zephyr’s fight wages on with Zephyr using his Battle Smasher to get the upper hand. Luffy, using all his might continues to punch Zephyr’s Battle Smasher until he breaks it. Zephyr removes the Battle Smasher and fights Luffy with only the usage of Haki. The two are still equally matched and in the final strike, they both knock the other one down. Zephyr admits defeat and believes that Luffy will now kill him (for he believes all pirates are the same), but Luffy spares Zephyr and says he doesn’t want to kill anyone. Seeing how Luffy is different from other pirates Zephyr realises the errors of his ways and understood that his actions were driven by anger, he apologises to Ain and Binz for all that he has done and asks for their forgiveness. In that moment, Kizaru and the navy appear and choose to execute Zephyr and the Neo Marines, as well as the Straw Har Pirates whiles they’re all weak from their previous battle. The Straw Hats prepare themselves for battle, but Zephyr walks forward, stating that he has done everything he wanted to do and now he will pay the price for his actions. Just then a wall of ice appears and separates Zephyr from the others, thus giving the Straw Hats, Ain and Binz the chance to escape, whiles leaving Zephyr to fight back against the marines. As the Straw Hats sail away, Zephyr battles against the marines until he succumb to his injuries and died. Ain and Binz mourn their loss, as they cry over a makeshift grave that used Zephyr’s Battle Smasher as the centrepiece. Kuzan tells them not to cry and states “he lived his life the way he wanted. Don’t you think he was amazing.” In the final scene of the film, it shows a young Zephyr dressed as a super hero fighting off a group of bullies who were harassing a girl. Zephyr beats the bullies with ease and as the bullies run away Zephyr states that he is the “hero of Justice” as he shouts the word “I’m Z” In a mid credit scene, the Straw Hats return to Dock Island, giving their gear and weapons back to Mobston, before going their separate ways.