The story begins with a young boy named Gon, who aspires to be a hunter just like his father Ging. Ging leaves his son in the care of Mito, Gon's aunt, and has not been seen since. Gon catches the local monster fish, "Lord of the Lake", in order to prove his ability to take the exam. Although Mito is reluctant to let Gon leave his home, she relents after he is determined to understand the reason his father left him and his interest of being a hunter.

Gon and Killua begin training in Hatsu, the culmination of everything they've learned about Nen. And finally, Gon challenges Hisoka to return the favor from the Hunter Exam.

After learning Nen and becoming a true Hunter, Gon returns to Whale Island with Killua. When he arrives, Mito has a box for him. She was told by Ging to give this box to Gon once he became a Hunter. However, it appears that the box cannot be opened.

The biggest auction in the world is about to take place in York New City. The Phantom Troupe leader, Chrollo, has instructed the members to gather in the city. For what purpose? The band of murdering thieves is about to make its move.

After Uvogin slaughters the Mafia's pursuit, the Mafia dispatches their secret weapon, the Shadow Beasts. However, Uvogin is able to defeat them by himself. During the battle, the spider tattoo on Uvogin's back is revealed, and Kurapika springs to action.

The anticipated battle between Kurapika and Uvogin begins! Can Kurapika really withstand Uvogin's abilities, and just what are the full extent of the powers in Kurapika's chains?

The auction has been rescheduled, and the Mafia expects the Phantom Troupe to attack again. The Ten Dons have hired multiple assassins to deal with the Phantom Troupe. Light Nostrade sends Kurapika to join the assassins in dispatching of the Troupe.

Kurapika has captured Chrollo. He offers to release Chrollo if Pakunoda brings Gon and Killua to him. However, Kurapika is unable to control his emotions in the presence of the Troupe leader.

The fight between Netero and the king comes to an end.

Pitou completes Komugi's treatment and Gon forces her to accompany him to Peijing in order to restore Kaito's mind, while Komugi stays behind with Killua and the others. Meanwhile, Pouf and Youpi reach the site of Netero's battle with Meruem and can't hide their feelings of sadness upon finding their king's maimed body.

A message of hostage exchange sends Welfin on the field. One moment he encounters Menthuthuyoupi, and the next, Shaiapouf finds Youpi lifeless. When he returns to the King, Meruem demands Shaiapouf's secrets. On their way, Shaiapouf unsuspectingly coughs out blood, just like how blood trickled from the King and Menthuthuyoupi.

Gon apologizes to Kite for not being strong enough to save him. Kite tells him they'll always be friends and that he should go get to know his dad. Gon returns to the Election Hall only to find a note that Ging has gone to the World Tree. Gon, Killua, and Alluka journey to the World Tree where Killua reveals Alluka's powers to Gon. Killua vows to protect his sister and says farewell to Gon, promising they'll meet again. Gon in turn promises to introduce Killua to Ging when they meet again.