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.

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.

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.

A female prisoner claim that Majitani is only unconscious, thus Kurapika's match has not been settled. Leorio, and even Killua cannot persuade Kurapika to finish the fight for the latter refuses to fight a person who has lost the will to fight. Frustrated, Leorio decides to use the majority rule as a way out of the difficulty but no one supports him. Elsewhere Hisoka is met by Togari, a former examiner whom Hisoka attacked and is now wanting revenge. Togari attacks with four crescent blades, only to be finished with one sweeping attack. Hisoka then becomes the first applicant to pass this phase. Meanwhile, the team suspects Majitani's real condition. The female prisoner challenges Leorio to have a betting game instead. Leorio agrees and bets ten hours that Majitani is alive, which he wins. Next, he bets twenty hours on Majitani feigning unconsciousness. To confirm, he brings Majitani to the edge of the platform and threatens to drop him. Seeing that, the prisoner changes her bet to forty hours on Majitani being conscious. When he is about to be dropped by Leorio, Majitani moves and admits defeat, putting the score at 2 - 1 in favor of Leorio's team. However, they only have 20 hours left to wager

The team stays inside a small room for fifty hours and keep themselves from getting bored. Then they spend the remaining time going to a series of traps and tricks. At the last room, they encountered two doors and are forced to either choose the long and hard path (45 hours) in which all of them may use or the shortcut (about 3 minutes) wherein two of them must be left behind. As disputes break out among them, Gon comes up with an ingenious idea of opening the long way and breaking through the wall to go to the shortcut so all five of them pass this phase.

Gon decides to send a letter to his aunt Mito in order to inform her about the events that had happened during his journey. He started to narrate the story on the events starting from the preliminary Hunter exam to the point when he met Leorio, Kurapika, Killua and the other examinees.

Gon learns to master his accuracy with his pole to try and steal Hisoka's number plate.Finally mastering it,He decides to steal it when Hisoka is busy catching his Prey.

Gon is relying on Bloodcrazy Butterflies to find his target, Hisoka, before waiting for the perfect time to use his skill with the fishing rod to snatch Hisoka's tag. Meanwhile, Leorio is tricked by Tonpa and loses his own tag, but Kurapika helps him recover it. Now that Kurapika and Leorio know that neither is the other's target, they decided to form an alliance.

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...

Gon and his friends have been trapped inside a cave by poisonous snakes. Bourbon, the person responsible for the trap, is already dead, and nobody knows how to disarm the trap. Meanwhile, Leorio, who was bitten by the snakes, is growing weak. Gon manages to get them out of the sticky situation and through to the final phase of the exam. But first, Netero wants an interview with each of the remaining applicants...

Gon and his friends have advanced to the final phase of the Hunter Exam. The final phase is a tournament where the winners are out and the losers advance. The rule is that if you kill your opponent, you'll be disqualified. The first mach is Gon versus Hanzo. Gon can't do anything against Hanzo, but he refuses to give up. Hanzo is losing his patience and threatens to break Gon's arm.

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.

Gon is upset that Killua was forced to kill. Gon is mad at Illumi and proclaims that he will go to Kukuroo Mountain to rescue Killua. As Gon and his friends depart, Satotz mentions that the Hunter Exam isn't over yet...

Gon, Kurapika and Leorio arrive at the Butler's Quarters, where the Head Butler entertains them while waiting for Killua. But just what game does he have in mind, and what are the stakes?

A letter from Gon arrives at Whale Island for Mito... (A recap of everything that has happened.)

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

After reaching the 200th floor, Gon and Killua run into Hisoka's barrier of Nen. They ask Wing to use the violent method for activating their Nen potential. As the deadline for registration draws near, they begin training in one of the four major principles of Nen, Ten.

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.

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.

Gon has fights against Gido and Riehlvelt coming up. He's still mad about what they did to Zushi. Gon is able to withstand Gido's attacks and overwhelm him in battle. This causes Hisoka to smile.

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 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.

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.

The auction is finally about to begin. Gon, Killua, and Leorio are working hard to amass enough money to buy Greed Island. Kurapika has been assigned to monitor the auction house. Meanwhile, the Phantom Troupe draws close. All paths will soon cross in York New City.

Kurapika was able to capture Uvogin, a member of the Phantom Troupe. Kurapika struggles to control his rage as Uvogin makes demands as though he isn't a captive. That is when Kurapika receives an e-mail from Hisoka...

Uvogin was able to escape with some help from his fellow bandits. However, after the blow to his pride, he is determined to track down and Kurapika and defeat him. Kurapika realizes that the Phantom Troupe has identified their location and moves the boss to a safe place while awaiting the Phantom Troupe's arrival by himself.

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 leader of the Phantom Troupe is dead... Kurapika is shocked by the news. Unconvinced, he tries to get a glimpse of the body. Meanwhile, the dead bodies of the other Troupe members have been discovered.

Gon, Killua, Kurapika, and Leorio are finally reunited. Kurapika reveals his Nen powers to the others. However, Killua is afraid that Kurapika is now in danger because one of the Troupe members can read minds. Meanwhile, Chrollo is using the fortune telling power he stole from Neon to tell the fortunes of the Troupe members.

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.

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...

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.

Killua returns after easily passing his second try at the Hunter Exam. Now that Gon, Killua, and Bisky are together again, they begin working on beating this game by collecting cards. Meanwhile, the other players are scheming to gather the cards they need to complete the game.

The condition for obtaining Patch of Shore is to chase a band of fifteen pirates out of town. Gon and crew are immediately taken to the boss, Razor, but they are quickly defeated. The plan is to recruit stronger party members and try again, so they start with the player named Chrollo.

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 is unable to hold onto Razor's throw and is sent to the outfield. He uses Back to return, but Hisoka is also injured and the situation looks grim. However, Gon has an idea for defeating Razor, but he needs Killua's help to pull it off.