The movie begins with Killua having a nightmare about his brother Illumi's warning to never make friends, claiming that eventually he will betray or get betrayed by them. He wakes up alongside Gon on an airship, where the former promises to never betray him. Upon arriving at their destination, they meet Leorio and learn that he and Kurapika were investigating a rumor about a survivor of Kurapika's Kurta Clan until they meet a young boy whom Kurapika recognized as his childhood friend Pairo, who attacks him and steals his eyes. Unconscious since then, Kurapika awakens beside the others and soon after he has visions through his stolen eyes of a man whose right palm is marked with a spider tattoo, the same used by the members of the Phantom Troupe.
Based on other details seen by Kurapika in his vision, Gon and Killua leave him under Leorio's care and split up in search for Pairo's location. Gon ends up meeting and befriending a young puppeteer called Retsu and when Killua reunites with him, they realize that Retsu is a girl. Because of Killua’s loyalty towards Gon, Killua quickly becomes jealous of her. When night falls, Leorio and Kurapika are approached by Hisoka while Gon and the others are attacked by Uvogin, who was presumed to be dead and saved by Nobunaga and Machi who defeat him. It is then revealed that Uvogin was revived as a puppet by Omokage, a former member of the Phantom Troupe who was defeated and replaced by Hisoka. Omokage sends a team of puppets including one based on Pakunoda to attack his former companions but they are all destroyed by them. After Omokage retreats, Nobunaga and Machi leave as well, warning Gon and Killua to not stand between Omokage and the Phantom Troupe as they have a score to settle with him.