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.

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.

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 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.

After hearing Bisky's lecture on rock-paper-scissors, Gon decides to work on a special technique modeled off of rock-paper-scissors by using Enhancer, Emitter, and Conjurer abilities. Meanwhile, Killua leaves the game temporarily to take the HUnter Exam. While he's gone, Gon and Bisky find learn about the Bomber's most recent attack.

As the king kills the ruler of East Gorteau and takes over the country, Gon and Killua return to meet Palm, prepared to face her fury upon failing to fulfill their promise, but she decides to forgive them when Gon accepts her request to have a date with her. After learning from Morel that they found Kite, Gon takes Palm for her date, while Killua keeps trailing them in case of an enemy attack, and his fears are confirmed when Rammot appears before him.

Shoot and Knuckle stay behind to fight Youpi while Morel rushes forward to face Pouf. While looking for Pitou, Killua turns back briefly to assist Ikalgo unaware that he accidentally put his friend's cover at risk.

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

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.