The movie begins with Killua dreaming about his brother Illumi's warning to never make friends, claiming that eventually he will betray or get betrayed by them. He wakes up along Gon on an airship. Upon arriving at their destination, they meet Leorio and learn that he and Kurapika were investigating a rumor about a survivor of Kurapika's Kuruta Clan until they meet a young boy whom Kurapika recognized as his childhood friend Pyro, who attacks him and steals his eyes. Uncounscious 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.

The strongest Hunters that once existed in the Hunter Association were split into "light" and "dark", and each walked down their respective paths. The "dark" side begins moving in order to massacre all Hunters! After a brutal attack from the "dark" side Hunters, Killua is injured and Kurapika is almost dead. What is the real goal behind the attack on all the Hunters? Now that the crimes of Netero & the Association are announced publicly. Will Gon take the dark side's path to find the necessary strength to save his friends? What actions will Gon take when the many crimes of Netero and the Hunter Association are unveiled...!?