The film opens with Killua Mariya Ise haunted by a nightmare about his brother Illumi's warning to never make friends, because such ties can lead to betrayal either way. He wakes on an airship beside Gon, and the two promise to stand by each other as they head toward their destination.
On arrival, they meet Leorio Keiji Fujiwara and discover that he and Kurapika Miyuki Sawashiro have been following a rumor about a Kurta Clan survivor. A boy appears—the child Kurapika once knew as Pairo—who attacks Kurapika and steals his eyes. Unconscious since the attack, Kurapika awakens and, through visions granted by the stolen eyes, glimpses a man with a spider tattoo on his right palm, the mark associated with the Phantom Troupe.
Gon and Killua split from Kurapika to search for Pairo. Gon befriends a young puppeteer named Retsu Aya Hirano, and when Killua reunites with him, jealousy flares at the new friendship. That night, Leorio and Kurapika are approached by Hisoka Daisuke Namikawa, while Gon and the others are attacked by Uvogin [Akio Otsuka], who is revived as a puppet by Omokage [Naohito Fujiki], a former Phantom Troupe member who seeks his own ends. Omokage sends a team of puppets—including one modeled after Pakunoda Romi Park—to strike, but Gon and his companions destroy them. Omokage retreats, and Nobunaga Naoya Uchida and Machi Rena Maeda depart, warning the group not to stand between Omokage and the Phantom Troupe, as they still have a reckoning to settle.
Next day, Retsu leads the group to the mansion that appears in Kurapika's vision. Leaving her behind for safety, they encounter another puppet—this time based on Illumi Masaya Matsukaze—which attempts to steal Killua's eyes. Gon intervenes and ends up having his own eyes taken instead. He explains that he sacrificed his eyes to help them track Omokage, and reveals that Retsu is also a puppet in his circle. Reunited with Leorio and Kurapika, they press on to Omokage's hideout.
Inside, Omokage reclaims his eyes from Retsu, who is revealed to be a puppet made from his deceased sister. When Gon and the others confront him, Omokage declares his aim to claim Leorio and Killua's eyes to empower his puppets. After confessing his role in the Kurta massacre and claiming there are no scarlet eyes left in his possession, Omokage unleashes dolls modeled on Pairo and Illumi. Gon and Kurapika, aided by Leorio and Killua, defeat the dolls and reclaim their eyes. Omokage then activates six more puppets based on Phantom Troupe members to attack; Hisoka arrives to fight alongside them. As the battle unfolds, Omokage absorbs the other three to gain their powers, and the group combines their efforts to restrain him with Kurapika's chains. Defeated, Omokage faces a choice: be spared if his powers are sealed for life. He refuses. Killua volunteers to kill Omokage in Kurapika's place, but Retsu suddenly stabs Omokage, claiming enough suffering has been caused. The real Phantom Troupe arrives but agrees to let Kurapika and Hisoka go for now, with a future showdown looming. As flames engulf the mansion, Retsu chooses to sacrifice herself with her brother, thanking Gon and Killua for the moments they shared. Sometime later, Gon and Killua part ways with their friends, continuing their journeys together.
