Twelve-year-old Gon Freecss one day discovers that the father he had always been told was dead was alive. His Father, Ging, is a Hunter — a member of society's elite with a license to go anywhere or do almost anything. Gon, determined to follow in his father's footsteps, decides to take the Hunter Examination and eventually find his father to prove himself as a Hunter in his own right. But on the way, he learns that there is more to becoming a Hunter than previously thought, and the challenges that he must face are considered the toughest in the world.
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.
As the deadline established by Netero approaches, the chairman and his companions continue to wipe out the Chimera Ant squads one by one. While the remaining squad captains discuss how to deal with the problem, the final member of the royal guard, Menthuthuyoupi, is born. Meanwhile, Gon and Killua complete their training and challenge Knuckle for real.
As the battle with Knuckle begins, Gon is told that his Janken technique is fatally flawed - but Gon exploits this weakness, countering as his opponent tries to take advantage. Just as Gon is about to deal a finishing blow, he collapses from exhaustion. With the deadline the next day, the final showdown is looming. As Gon sleeps, Biscuit spars with Killua, after which she explains the nature of his own weakness. She issues an ultimatum - should he lose the next day's battle, he must leave Gon's side.
Gon and Killua are finally facing off against Knuckle and Shoot. Killua takes Shoot while Gon's opponent is Knuckle. Gon succeeds in sensing Knuckle through his aura, but then LoanBoy pops up on his left arm. Meanwhile, Killua is struggling against Shoot.
At long last, the Queen gives birth to the King. The Chimera Ants are cowed by the menancing aura emitted by the King. Pitou, Pouf, and Youpi kneel before the King to greet him, but with that gesture, they have abandoned the Queen.
Despite all efforts to save the queen, she does not resist her wounds and dies, but not before revealing to Colt the name she had chosen for the king, "Meruem". A final live offspring is found inside her body and Morel offers himself to protect both after he promises that they will never eat humans anymore. As the other squad leaders leave to build their own colonies, the king and the royal guard arrive at the neighboring country of East Gorteau.
As the king kills the ruler of East Gorteau and takes over the country, Gon and Killua return to meet Palm, prepared to face her fury upon failing to fulfill their promise, but she decides to forgive them when Gon accepts her request to have a date with her. After learning from Morel that they found Kite, Gon takes Palm for her date, while Killua keeps trailing them in case of an enemy attack, and his fears are confirmed when Rammot appears before him.
Divided between his drive to flee and his will to protect Gon, Killua find himself in a dire situation until he realizes that he is under the effect of one Illumi's needles, easily killing Rammot after he breaks free fom it. Meanwhile, Gon's date with Palm turns to the worse when he claims that he can't stay by her side. As shoot returns to check on them, morel and Knuckle confront Cheetu, one of the Chimera Ants on the run.
After a brief fight with Cheetu, Morel and Knuckle return to check on Gon and Killua as they finally reunite with Kite, but upon seeing that he was turned into a mindless rogue by Neferpitou, Gon swears to avenge him. The Hunters then travel to East Gorteau, where the government summons all the population to meet at the capital for an undisclosed event in ten days. Knowing that it is all a plan of the Chimera Ants, Netero contacts the others and they start making plans to confront the king and the royal guard in the night preceding said event.
As news about the rogue Chimera Ants spread arround the world, six members of the Phantom Troupe appear at Meteor City to wipe out some of them which had established a colony there.
The Phantom Troupe reaches Zazan, the leader of the Ants, eliminating all oposition on the way. Fighting Zazan by himself, Feitan is forced to unleash his true power against her, which is feared even by his companions.
Once inside East Gorteau, Gon and Killua take separate ways in preparation for the attack on the palace, but once alone, it does not take long for Gon to be attacked by Ants sent by Meleoron whose presence is concealed thanks to his Chameleon-like powers.
As Gon deals with his enemies, Killua tries his best to save the citizens of nearby villages from falling prey to the Chimera Ants' scheme until the Government, under the Royal Guards' control, declares martial law to hinder his plans. Meanwhile, Shoot and Knuckle detect Cheetu's presence and attempt to intercept him.
Leol's party is sent by the Royal Guard to stop Killua's interference and Meleoron is found out by Gon, but instead of fighting, the Chimera Ant attempts to reason with him while hiding his true intentions.
Killua confronts Ikalgo but later, saves him from getting eaten by his own subordinates. The Ortho Siblings confront Killua in their game, a 1-501 dart game where he gets continuously attacked. After feigning death, Killua beheads his opponents in a flash, but he collapses due to extreme blood loss and Ikalgo decides to repay the favor by taking him to be treated.
Gon becomes friends with Meleoron, who in return reveals the true extent of his powers and the reason why he wants the king dead. As the Hunters make adjustments in their preparations to storm the palace, the king entertains himself with board games until an unusual player appears before him.
Despite having mastered the rules of the board game "Gungi", the king is upset for still being unable to defeat the champion before him. Meanwhile, Morel is approached by Cheetu who uses his new abilities to trap him inside a closed space, claiming that he can't leave unless he manages to catch him in 8 hours.
As the king is yet to defeat his opponent, Cheetu tries to provoke Morel into running after him with no success, unaware that he is setting a trap for him. Meanwhile, Knov realizes the enemy's trick to detect him and comes with countermeasures against it.
The king attempts to intimidate the Gungi champion but moved by her determination, he rips off his own arm as a form of apology. With Neferpitou using her powers to treat the king, the palace's defenses are lowered and Knov rushes to sneak inside it in preparations for the hunters' attack. Meanwhile, Palm prepares to infiltrate the palace as well.
Knov succeeds in his mission to breach the palace's security, but just feeling the proximity of Royal Guards' overwhelming aura is enough to drive him into despair. Palm takes advantage of the lecherous secretary Bizelf to infiltrate the palace as well and Morel is confronted by the Chimera Ant Leol, who fights using the powers of those who owe him a favor.
Even with his borrowed powers, Leol has been defeated by Morel while Killua recovers from his wounds and invites Ikalgo to join his side. Meanwhile, Palm starts her investigation when a massive and ominous aura surrounds her.
Gon and his friends make the final preparations for their assault on the palace. Meanwhile, the king is yet to defeat Komugi, the Gungi champion and when he decides to kill her, he ends up protecting her instead, for reasons that even he can't explain.
The time has come for Gon and his friends to infiltrate the palace and confront the Royal Guard, who are making preparations for the upcoming selection. As his concerns about Komugi increase, the king starts questioning his own existence and purpose.
The selection is at hand, but the king starts isolating himself from his servants, including the Royal Guard. Meanwhile, Gon's party is about to break into the palace.
The Hunters assault on the royal palace begins. Gon and his friends break inside and come across Menthuthuyoupi, while Netero and Zeno strike from the sky and Neferpitou jumps up to confront them, just to be driven away when the chairman makes a small demonstration of his powers.
Gon's party confronts Youpi while Pouf and Pitou rush to the palace to assist the king, who is distraught with Komugi's condition as she gets herself badly injured during the attack.
Shoot and Knuckle stay behind to fight Youpi while Morel rushes forward to face Pouf. While looking for Pitou, Killua turns back briefly to assist Ikalgo unaware that he accidentally put his friend's cover at risk.
Separated from the Royal Guard, the king departs from the palace with Netero to have their fight elsewhere and Gon, learning of Pitou's location, steels himself to confront it. Meanwhile, Pouf enters in a cocoon in preparation to confront Morel, and Shoot fights Youpi to the limit of his forces until Knuckle steps in to protect him.
The disguised Ikalgo reaches the lower levels of the palace to look for Palm, unaware that he is being followed. Meanwhile, Meleoron leaves Knuckle's side and proceeds further into the palace, but another Chimera Ant, Welfin, tracks his smell. Elsewhere, Gon and Killua find Pitou, who is too busy to fight them while tending to Komugi's wounds.
Face to face with Pitou, Gon can't hold back his rage and urges the chimera to fight him. Realizing that Pitou is willing to sacrifice itself to protect Komugi, Killua attempts to calm down his friend down with no success, but in the end, Gon gives one hour for Pitou to treat Komugi in exchange of accompanying him to meet Kite and help him recover his senses.
Cheetu attempts to provoke Zeno into fighting him, but Silva appears to pick up his father, killing the ant instanly in the occasion. Separated from the others, Youpi realizes that he failed to prevent the intruders from approaching the king and attempts to vent out his anger on Knuckle and Shoot, creating an overwhelming explosion, a feat that surprised even himself. Knuckle believes this could prove itself as an opportunity to make a comeback, while Youpi plans to use it to defeat them for good.
Ikalgo infiltrates the palace's lower levels to look for Palm with no success. While returning to the surface, his cover is blown and he finds himself trapped in the undergound with an enemy. Meanwhile, Youpi pretends to be angered in order to have Knuckle falsely believe there is an opening for him to attack. Youpi's plan works, but just before he could kill his opponent, Killua paralyzes the ant with a lighting bolt and steps in to fight him.
Taking advantage of Youpi's distraction, Killua vents out his anger by beating him up, but is forced to flee after his lighting power runs out. Meanwhile, Ikalgo makes use of the underground security system to outsmart his pursuer and find a way to escape back to surface. Morel, on the other hand, is in doubt about whether he should make the first move against Pouf or not.
Morel decides to make the first move and unwillingly frees Pouf from his restrain. Upon realizing that Shoot is missing, unaware that he was taken by Knov to be treated, Knuckle confronts Youpi, assisted by Morel, whose options are drastically reduced upon having his pipe stolen by Pouf, who after realizing that the king is nowhere to be found, decides to rejoin Pitou, who is still working to stabilize Komugi under Gon's vigilant eyes.
Knuckle and Morel confront Youpi with their lives on the line, but just a few moments left of neutralizing his nen with his ability, he is forced to abandon his master or give up on defeating his oponent.
Far away from the palace, Netero prepares himself to confront the king, who much to his surprise, recognizes his value as a fighter and is not willing to kill him. Meanwhile, Pouf learns the situation from Pitou and sneaks past Gon's vigilance to rejoin Youpi as they leave the palace to search for the king.
Ikalgo is attacked by Welfin but the enemy's attempt to restrain him backfires and they find themselves in a stand off. In the occasion, Welfin regains some of his lost memories from when he was still human and gives him a hint regarding Palm's location.
Killua meets Palm and learns that she was transformed into a Chimera. Refusing to let her see Gon in fear of what effects this could have on his already unstable mind, Killua is attacked by her, unaware that she is under Pouf's control.
Netero convinces the king to fight him by revealing that he will tell him his true name once defeated. The chairman then unleashes his most powerful technique that despite striking the king countless times, olny manages to scratch him.
The fight between Netero and the king comes to an end.
Pitou completes Komugi's treatment and Gon forces her to accompany him to Peijing in order to restore Kaito's mind, while Komugi stays behind with Killua and the others. Meanwhile, Pouf and Youpi reach the site of Netero's battle with Meruem and can't hide their feelings of sadness upon finding their king's maimed body.
Pouf and Youpi sacrifice most of their own bodies to heal Meruem, who rises stronger than before, but with most of his memories missing. Pouf then decides to take this opportunity to dispose of Komugi in hopes that Meruem never remembers about her at all, but is attacked by the other hunters, who realize, much to their horror, that the king is still alive and is about to return to the palace.
Shaiapouf's plan to kill Komugi is thwarted when Killua faces him in a battle of words and speed. When the King arrives in the palace, Shaiapouf is resolved to get rid of the Gungi board before the King can remember anything else. Finally, Neferpitou and Gon arrive at the place of their long-awaited battle.
Shaiapouf continues his plan to remove anything that could trigger Meruem's memory of Komugi as the King arrives at the palace. Killua continues to hold onto Komugi, and meets with Palm. Gon and Neferpitou arrive where Kite is, however, Gon must now face the truth.
After telling gon the truth about kite, Pitou tells gon that she is sorry for what she did, but it's too late for apologies.
The King still struggles to retrieve his memories as he and his two remaining Royal Guards return to the palace. He eventually knocks out Meleoron and Knuckle Bine with his En, and later engages Shaiapouf and Menthuthuyoupi in a race against time. Meanwhile, only two remain, Palm and Ikalgo, and hide an unconscious Komugi underground.
A message of hostage exchange sends Welfin on the field. One moment he encounters Menthuthuyoupi, and the next, Shaiapouf finds Youpi lifeless. When he returns to the King, Meruem demands Shaiapouf's secrets. On their way, Shaiapouf unsuspectingly coughs out blood, just like how blood trickled from the King and Menthuthuyoupi.
Meruem uses his final permissible En and enlightens his surrounding with that and approaches to Welfin who was not detected by his En earlier. Caught between the desire to live and avoidable death, Welfin finally utters the name of Komugi and the secret Shaiapouf was trying so hard to protect now is finally revealed with Meruem regaining all of his memories about Komugi.
Now knowing his fate, Meruem admits defeat and reveals that all he wants now is to spend his final moments playing with Komugi, convincing Palm to tell him where she is hidden. East Gorteau and the NGL gets in turmoil after the fall of the Chimera Ants and the Hunter Association start making preparations to decide who will succeed Netero as its president. Despite knowing that she will also be poisoned to death by staying close to Meruem, Komugi stays by his side until his last breath and passes away in sequence.
After the fall of the king, the remaining Chimera Ants move on with their lives, each following their own path. However, Gon is still in critical condition after his battle with Neferpitou and Killua departs in search for a way to heal his body. Meanwhile, the top members of the Hunter Association, the Zodiacs, assemble to organize the election to choose the next president, following the will of Netero's last message.