Gon, a young boy who lives on Whale Island, dreams of becoming a Hunter like his father, who left when Gon was still young.
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.
