With the navigators' help, Gon, Kurapika and Leorio arrive at Zaban City, the venue of the exam. The navigator leads them to a small restaurant, which is revealed to be the front for the venue. Gon's group is led to an elevator disguised as a back room, which leads a hundred floors underground. Below, they meet the rest of the participants and given their numbers. There they meet Tonpa, a regular participant who claims to have tried and failed 35 times in the exam.

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.

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.

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 Troupe is attacking the auction with all their power. The Ten Dons hired assassins are no match, except for Zeno and Silva.

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 wakes up, and finds himself being congratulated by Satotz for being the first person to pass the Hunter Exam. Gon asks Satotz if the Exam was still going on, and Satotz tells him that it's over. Satotz reveals what happens after he lost consciousness, and Gon finds out some shocking turn of events.

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.

While following Satotz, a fog moves into the swamp and most of the participants are either rendered unconscious or killed by traps and verocious beasts. A group of candidates target Hisoka as they feel he's a threat. Gon and Killua are separated from Leorio and Kurapika and both sides are eventually attacked by monsters. Leorio and Kurapika encounter Hisoka about to be attacked by candidates but are shocked to watch the magician easily take the candidates down. Hisoka then targets Leorio and Kurapika, but realizing that they are no match for him, they decide to head in different directions to stop him from following. However, Leorio returns, unable to run away from a fight. As expected, Leorio is beaten badly by Hisoka. Before the melee can get any worse, Gon, who is separated from Killua, arrives to stop Hisoka. Although he is also no match for Hisoka, he manages to hit his face once before being strangled by Hisoka.

All the candidates are told by Beans, Neteros' secretary to get their dinner and rest and prepare for the third phase the next morning. Tonpa tries to commit sabotage again by trying to keep Kurapika and Leorio awake for the whole night, but is exasperated to find that none of them fall for his tricks. Gon and Killua explore the airship, and Killua tells Gon that he is actually from a family of assassins. He wished to strike out on his own, which his family has not taken lightly. Neteros arrives and tests both boys' instinct and asks how they felt about the difficulty of the exam. Neteros invites both of them to a game, whoever can grab the ball he is holding before dawn will immediately pass the exam. Gon and Killua find it too hard to pass up, but discovers that with Neteros' skills, they are unable to grab the ball. Eventually Killua realizes that with their skills, they will never be able to take the ball from Neteros for a year, if he keeps it up.

Kurapika and Leorio are being stalked by Hisoka, but they managed to negotiate their way out of a fight. However, the encounter leaves Hisoka aroused, so he leaves in search of a new target. Gon is able to use his fishing rod to snatch Hisoka's tag right when Hisoka attacks his target. However, as Gon tries to escape, he is attacked by another applicant and loses his tag...

Kastro has used his ability to create a clone of himself with Nen to sever Hisoka's arm and take an advantage in the fight. However, despite losing both arms, Hisoka appears to be perfectly calm. Kastro loses his cool and attacks Hisoka.

After landing a punch on Hisoka, Gon returns the tag from the Hunter Exam. Hisoka is ecstatic to see Gon's development and uses his own Nen to attack. Gon is scared, but he recklessly continues to attack! Will he emerge victorious.

Gon and his friends are hoping to win the reward that's been placed on the Phantom Troupe. At the same time, Machi and Nobunaga have been dispatched to search for the "chain user" because Uvogin hasn't returned. Gon and Killua receive a tip and begin shadowing the two Troupe members.

Gon and Killua have been captured by the Phantom Troupe. They are questioned about the chain user that the Troupe is searching for, but the two of them don't know that the chain user is Kurapika. As they're about to be released, Nobunaga decides to keep them around as potential recruits for the Troupe.

The Phantom Troupe has learned that Kurapika was the one who killed Uvogin. It's only a matter of time before they realize that the captured Gon and Killua are working with Kurapika? Chrollo takes Gon and killua to the hotel lobby, where Paknoda and the other Troupe members are waiting. Suddenly, the lights go out. Gon and Killua try to escape in the darkness. But Chrollo is the one who has vanished...

Gon, Kurapika and Leorio reach Dolle Harbor and are given instructions by the captain to head for the cedar tree on the hilltop behind the city. Moving through a small town, the three are stopped by a group of people, where an old woman gives a question requring them to choose from two choices. Answering wrongly, refusing to answer or attempting to head back will result in failure of the exam.

During the first test, a number of participants fall out from fatigue after running for at least forty kilometers. Leorio almost gives up until he is encouraged by Gon, who waits for him. Killua, a participant, is introduced and he is curious of Gon's personality when he discovers that the boy is the same age as him. Kurapika and Leorio talk about the reason for being a hunter, with Kurapika wanting to take down the Phantom Troupe as his clan was massacred by them for their precious scarlet eyes, which manifest when the Kurta uses their heightened sense. Leorio aims to be a hunter for money, for purely altruistic reasons, as his childhood friend died of an illness without the funds to save him. He wishes to be a doctor so he can give his patients free treatment. Finally, the participants reach the end of the tunnel they are in and up to the surface to the Numere Wetlands, also known as Swindlers' Swamp.

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.

Tonpa promptly gives up even before Bendot land a punch on him. Leorio is furious at what he has done but Tonpa tells them that his real plan is to sabotage rookies like them. Gon then faces Sedokan, who proposes a match to see whose candle burns the longest. Gon chooses the longer candle, unaware that it is oil-soaked, and his candle starts to burn faster midway. Seeing that his candle is not susceptible to strong winds, he puts it down and sprints towards Sedokan to blow his candle. The next match is between Kurapika and Majitani, who proposes a death match without weapons and and with the condition that one must die or surrender to finish the match. Majitani, who relies on scaring and intimidating his enemies to make them surrender, is easily defeated by Kurapika when he sees something in Majitani and makes him see red.

Gon and Killua arrive at the Heavens Arena and begin to work their way up, making a new friend, Zushi, who is trained in the martial arts.

While working to understand Nen and Ren, Gon and Killua run into a familiar acquaintance.

Gon faces the Nen user Gido in his first 200s Heavens Arena match. Gon uses Ten to protect himself, but he soon finds himself on the defense against Gido's Dancing Tops. As Gon desperately tries to find a way to fight back, he makes a bold decision...

A month has passed since Gon was seriously injured, and Hisoka and Kastro are about to fight in Heavens Arena. Kastro was able to knock Hisoka down in the past and sounds very confident in his interview. Hisoka appears unperturbed by the upcoming fight.