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?

Gon and Killua have finally realized Biscuit's true strength and asked her to teach them Nen. With that said, they begin their hard training.

Gon and Killua are gradually improving their Nen under Bisky's tutelage. They are now able to easily capture the monsters that they previously struggled against. While their training draws to an end, the Bomber is paying a visit to the players who have teamed up.

After hearing Bisky's lecture on rock-paper-scissors, Gon decides to work on a special technique modeled off of rock-paper-scissors by using Enhancer, Emitter, and Conjurer abilities. Meanwhile, Killua leaves the game temporarily to take the HUnter Exam. While he's gone, Gon and Bisky find learn about the Bomber's most recent attack.

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.

Team Genthru now has 96 different types of restricted slot cards after tricking Team Tsegzerra. Gon and Killua receive an invitation from other players to team up to prevent Genthru from beating the game. They head to Soufrabi to monopolize Patch of Shore, one of the cards Genthru is missing.

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.

Gon, Killua, and Hisoka team up to catch Razor's strongest throw. They're taking Razor head on. Once the ball has been secured, Gon uses all of his strength to launch it at Razor. The game of dodgeball is drawing to a close.

In order to beat the game, the other players must face off against Genthru. Tsezgerra offers to distract Genthru for three weeks. While Gon trains hard, Team Tsezgerra leaves the game temporarily to delay Genthru, but Mr. Battera has an unpleasant surprise for them.

Tsezgerra's tea has not returned to the game. Genthru finally turns his attention to Gon's group. Gon faces off against Genthru, Killua is against Sub, and Bisky takes Bara.

Genthru has shown that he is much stronger than Gon. However, after Gon refuses to back down, he finally uses Little Flower to severely injure Gon.

After defeating Genthru and collecting 99 restricted cards, Gon and his friends participate in the final event, a quiz tournament open to all players. After winning, Gon receives Ruler's Invitation.

Gon and Killua use the cards they brought back from the game to warp to Nigg, who they believe is Ging. However, they are sent to a completely different man who immediately knocks them to the ground. However, Gon finds him familiar for some reason.

Gon and Killua join Kite's team as they investigate the Chimera Ants. The Chimera Ants are dangerous insects that can pass traits from the prey they consume to their offspring. As Kite begins to fear the worst, the Chimera Ants begin to feed on humans.

Kite uses the location where the Chimera Ant arm was discovered and ocean patterns to determine where the actual Chimera Ant is. It turns out to be an isolated country that bans all forms of technology. Meanwhile, the Chimera Ants continue to evolve.

After passing a strict border checkpoint, Gon and his new friends enter NGL where they suspect the Chimera Ant is. However, ten other teams of Hunters have already arrived before them. Meanwhile, the Chimera Ants, with their new names and individual personalities, are attacking humans.

Pokkle and Ponzu use Ponzu's bees to deliver messages asking the Hunter Association to help eliminate the Chimera Ants. Meanwhile, the Chimera Ants have attacked Gyro, the shadowy ruler of NGL, and taken his guns. As the situation gets worse, Ponzu's message reaches Gon's group.

Gon, Killua, and Kite discover the remains of a destroyed village. There, they encounter their first Chimera Ant. Gon and Killua are shaken by the speed and power displayed by the Chimera Ant. However, Kite tells them that they must defeat the Chimera Ant or leave.

Some of the more aggressive Chimera Ants have eaten the villains who ran the NGL underground and grown increasingly evil. When Gon looks away from their gruesome act, Kite admonishes him. Now, they must battle for their lives. Meanwhile, a Chimera Ant is on the verge of discovering Nen.

The Hunter Association has dispatched an expeditionary force to exterminate the Chimera Ants. Meanwhile, Gon and his friends are being targeted by Chimera Ants who seek to eat rare humans. They are forced into one-on-one battles with Chimera Ant captains. They easily dispatch their opponents, but Kite continues to feel uneasy. less.

As Gon, Killua and Kite approach the nest, one of the Chimera Ant Royal Guards, Neferpitou, awakens. Upon extracting information from a surviving Hunter, Neferpitou learns the secrets of Nen, including the means to awaken and control it.

As the Chimera Ants are reunited to unlock the power of Nen into their bodies, Neferpitou feels the presence of Kite approaching and leaves to confront him. Realizing that the enemy is too powerful for them, Kite warns Gon and Killua to flee, but Gon is taken by rage upon seeing Kite's arm being severed by Neferpitou and Killua is forced to knock him down and escape carrying him. After escaping the NGL, with Gon still uncounscious, Killua is approached by Chairman Netero who is sent there to wipe out the Chimera Ants assisted by two other Pro Hunters, Morel and Knov.

Gon and Killua meet Knov's student Palm and learn that to earn a place in the Extermination Squad and return to the NGL, they must win against Morel's students Knuckle and Shoot in one month. To increase their chances of winning, Palm asks for Biscuit's help and they start a harsh training routine with her. Meanwhile at the Chimera Ants nest, Shaiapouf, the second Royal Guard awakens.

After completing their training, Biscuit sends the exausted Gon and Killua to face Knuckle. Looking at the condition fo their opponents, Knuckle boasts that they could never move him an inch and bets his token on it. However His assumptions are proven wrong when Gon manages to land a powerful hit that knocks him out cold, and after awakening, Knuckle agrees that he will help them with their training until the deadline for returning the token comes. Meanwhile at the nest, Neferpitou focuses herself into reviving Kite for a second chance to fight him and Netero's team starts taking down small groups of Chimera Ants that bring the attention of the captains, while the king grows strong inside the queen's womb. As Gon and Killua spend their days training with Biscuit and sparring with Knuckle, Shoot, the second of Morel's disciples make plans about how to deal with them.

To ensure that Netero's last wish will be followed, Ging convinces the other members of the Zodiacs to procede with the election according to some rules defined by him. However, after the first round of voting, a winner is not decided and a second round begins. Meanwhile, Illumi informs Hisoka about Gon's condition and asks for his help to ensure Killua's safety as well, in a plan that somehow involves a fifth, yet unrevealed member of the Zoldyck siblings.

With the elections in a stalemate, Pariston, the current vice-president proposes a new set of rules to his fellow Zodiacs in order to solve the impasse, but the others know that he actually plans to make use of this to secure a victory for himself. Meanwhile, Killua returns home and asks his father to let him see his younger sister Alluka, intending to use her mysterious and frightening power to grant wishes in order to save Gon's life.

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.

Leorio's confrontation with Ging earns him the respect of his fellow Hunters and make him one of the frontrunners for the election. Meanwhile, Illumi begins an attack on Killua as part of his plan to kill Alluka, assisted by Hisoka, who has other plans for her.

Gotoh is killed by Hisoka, while the other butlers keep following Killua until he manages to shake them off. Meanwhile, Illumi uses his needles to take control of several people to assist on his plans and when news of it come to the Association, a team of Hunters is assembled to bring him to justice, while some of them decide to take advantage of it in order to win the election.

The election proceeds without a winner determined yet, and Killua is cornered by Illumi, who demands him to reveal which secrets he is hiding regarding Alluka's powers. Meanwhile, Hisoka keeps murdering other hunters just to amuse himself.

With only four candidates left, the election draws to its conclusion and has an unexpected turn when Leorio receives the support from two of the other remaining contestants, who are eager to prevent Pariston from winning. Meanwhile, Killua and Alluka finally arrive at the hospital where Gon is being treated.

Leorio is about to win the election, but loses all motivation to continue after a fully healed Gon appears before him, thanks to the power of Alluka, opening the way to Pariston's victory. Surrounded by his friends and the other hunters who celebrate his recovery, Gon meets his father at last.

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.

Gon climbs to the top of the World Tree where Ging is expecting him, and the two finally have a heart to heart. In this occasion, Ging reveals his intentions to explore the world beyond the current boundaries known to mankind and Gon tells him of all his adventures, while his friends keep following their separate ways, each one of them with their own dreams and goals to pursue.