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, 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.

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.

Gon and Kurapika reunite with Leorio and Killua at the Phase Two site. Satotz leads what remains of the candidates to meet the second phase examiners, named Menchi and Buhara. The examiners declare the next phase is to test their cooking skills, much to the candidates' disbelief. The test requires pork, so the candidates are sent to find pigs in the forest. However, the pigs living inside the forest are carnivorous and tear through the candidates. Thanks to Gon, they discover the pigs' weakness and they manage to each get one for their cooking. Upon tasting the candidates' cooking, Buhara gives a pass but Menchi fails all of them. Knowing the candidates will riot, Satotz informs Chairman Netoros of the Hunter Selection Committee to make an appearance. Netoros arrives to correct Menchi's habit of getting biased whenever it's related to cooking. Netoros allows Menchi to stay on as examiner, and she gives the candidates a retest: boil eggs laid by spider eagles on Mt. Split-in-Half.

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.

The airship reaches Trick Tower, the Phase Three site, which is a tall featureless pillar built on an equally high platform. The candidates are told that to pass Phase 3, they have to climb down from the top to the base of the tower. An experienced rock climber candidate tries to climb down but is eaten by some flying monsters. Later, Kurapika finds that more than half of the candidates have discovered hidden doors to go inside the tower, which Gon finds one as well. However, the catch is that there are many hidden doors, each one can be only used once and only one person can fit through a door, which means they have to split up. When they try out different doors, they realize that they end up in the same room. In the room, Gon's group are given instructions and special wristwatches for five of them to follow the majority, but they cannot proceed without a fifth member. Lippo, one of the Phase 3 examiners tells them this while explaining they have chosen the path of majority rule.

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.

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

After winning the bet about Majitani, Leroute, as what the prisoner is named, bets with Leorio about her gender. Despite looking conspicuously female, Leorio, much to Killua and Kurapika's annoyance, bets that she is male. Leorio thinks that team wins if he is correct; and if he is wrong, he will be able to touch Leroute to confirm. Leorio is wrong and goes on to check Leroute. Leorio then challenges Leroute in rock, paper, scissors, and loses. Killua then faces the feared mass murderer Johness the Dissector. Killua rips Johness' heart in an instant and even have it covered in a piece of Johness' cloth. The latter pleads for his heart, and Killua returned it after he is dead. The team thus gathers three points and pass the trial, but they are forced to wait the 50 hours that Leorio has lost with his bets in a small room. Meanwhile, applicants Gittarackur and Hanzo become the second and third one to finish the third phase.

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...

Killua grows tired of having Imori shadowing him so he challenges Imori to a fight and quickly dispatches him. Meanwhile, Gon has joined up with Leorio and Kurapika. The three of them devise a plan for taking Ponzu's tag and track her down to a suspicious-looking cave. That is when Leorio insists on heading in alone.

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, Kurapica, and Leorio arrive at Kukuroo Mountain only to find out that they cannot get close to the Zoldyck family estate. The Zoldyck family owns the mountain and all of the surrounding forest and the entire region is gated shut. There is a guard outpost immediately outside of the gate, but instead of serving as a guard, the man working in there actually cleans up the mess created by the watchdog whenever there are intruders into the grounds. Gon, unwilling to give up on "rescuing" Killua, learns from the gatekeeper that the actual door is the massive stone gate and anyone who enters via that path will not be attacked by the watchdog. Leorio tries to pull and push on the gate, to no avail. The gatekeeper informs them that the gate opens up different amounts of stone slabs based only on the strength of the person; however, the least amount of strength anyone needs to open the smallest portion of the door requires two tons of strength on each side.

Gon and his friends have decided to pass through the Trial Gate to see Killua. First, they must train in the servants' residence until they can open the gate. Meanwhile, Killua has learned that Gon and the others are here to see him. Gon, Leorio, and Kurapika are able to open the gate after completing their training, but the apprentice butler Canary stands in their way.

With help from Canary, who is concerned about Killua, Gon and his friends are getting closer to the mansion. However, Kikyo tells them that Killua cannot see them as he is in solitary confinement. Meanwhile, Killua has been summoned by Silva and asked if he wants to see his friend? Killua answers truthfully, and he is allowed to go see his friends...

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?