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.

Kurapika and the other job candidates have to battle their way out of the employers mansion... if they ever hope of obtaining any of the items they even need for the job.

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.

After Chrollo tells fortunes for all of the Troupe members, they suspect that Hisoka has betrayed them. Hisoka's desire to fight Chrollo drives him to take a big risk by altering his own fortune. Meanwhile, after learning that the Troupe is still alive, Kurapika teams up with Gon and friends and work on a plan to capture Pakunoda.

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.

Gon and his friends have teamed up with Hisoka and Goreinu to challenge Razor again. To round out the party, they recruit Team Tsezgerra. Their preparations allow them to breeze through the first few matches, but then Razor challenges them to a game of dodgeball.

Gon's party confronts Youpi while Pouf and Pitou rush to the palace to assist the king, who is distraught with Komugi's condition as she gets herself badly injured during the attack.

Netero convinces the king to fight him by revealing that he will tell him his true name once defeated. The chairman then unleashes his most powerful technique that despite striking the king countless times, olny manages to scratch him.

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

The King still struggles to retrieve his memories as he and his two remaining Royal Guards return to the palace. He eventually knocks out Meleoron and Knuckle Bine with his En, and later engages Shaiapouf and Menthuthuyoupi in a race against time. Meanwhile, only two remain, Palm and Ikalgo, and hide an unconscious Komugi underground.

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.

Killua reunites with his sister Alluka and uses her as a leverage for them to be allowed to leave the Zoldick state, as her powers can only be used to heal Gon if she is close to him. Meanwhile, Illumi asks for Hisoka's help to stop Killua's plans, and with elections yet to reach a conclusion, the Zodiacs keep arguing about a possible way to bring it to end.

Killua is allowed by his family to leave the Zoldick estate with his sister, but only under supervision of several butlers with orders to bring them home if he ever leaves Alluka's side or allows any of their secrets to be leaked. Meanwhile, Leorio appears and confronts Ging, asking him why he had not ever paid a visit to Gon at the hospital yet.

Gon apologizes to Ging for failing to save Kite and his father instructs him to apologize to Kite himself instead, affirming that he will wait for him to return. Meanwhile, Pariston wins the election, but renounces in favor of fellow Zodiac Cheadle and Killua seals Alluka's powers away to ensure that he can live a normal life beside him.

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.