Hunter Exam Story Arc
In the first major story arc, Gon takes a series of bizarre tests to become a Hunter himself, which include such things as navigating a deadly jungle, hunting other applicants, killing a wild boar, an extraordinarily long underground marathon and making sushi. During the Hunter Test, Gon meets and befriends three of the other applicants, Kurapika, Killua and Leorio.
Another of the applicants in the Hunter Test is Hisoka, a complex villain who uses playing cards as weapons, and who views Gon as an "unripe fruit" that he will take great pleasure in killing once he's grown up enough to present a challenge.
Zaoldyeck Family & Celestial Tower Story Arcs
The second story arc involves Gon, Kurapika, and Leorio springing Killua from his parents' mansion. At the end of the second story arc, Leorio leaves for medical school and becomes a professional doctor while Kurapika leaves to find work, taking both characters out of the story. In the third story arc, Gon and Killua go to the Celestial Tower (also known as "Heavens Arena"), a 251-floor building where people can compete in fighting tournaments around the clock for cash. It is here they meet the Kungfu master Wing, who teaches them about Nen, a chi-like energy that can be used to manifest superhuman powers. He teaches a young child named Zushi, who joins Gon and Killua to fight in the tournament to gain money and experience. Hisoka defeats another powerful Nen user, Kastro, who was able to create and use a double made from Nen. Hisoka loses both arms in the battle but Machi, a fellow Nen user and Genei Ryodan member, uses her ability to sew the arms back on. Gon battles Hisoka and is able to land a few hits but loses in the end.
Genei Ryodan Story Arc
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Main article: Genei Ryodan
The fourth story arc reunites the four main characters for the world's largest auction in a sprawling metropolis called Yorkshin City. While Gon, Killua, and Leorio try different methods to make enough money to buy Greed Island, a "Joystation" video game that could help Gon find his father, Kurapika takes center stage. This story arc introduces the Genei Ryodan (also known as the Phantom Brigade), a group of thieves who, among many other crimes, slaughtered all the other members of Kurapika's clan. Kurapika crosses paths with them while working as a bodyguard for a teenage girl named Neon, who has a clairvoyant Nen ability. He spends the rest of the arc balancing his bodyguard duties with his goal to hunt down the Genei Ryodan.
By the end of the Genei Ryodan story arc, Kurapika has directly killed Uvogin, indirectly killed Pakunoda (via a deadly Nen ability which killed her when she broke the conditions he had set onto her), and "sealed" Kuroro Lucifer's Nen ability (via the same ability he used on Pakunoda). The latter two are accomplished via an unsteady alliance with Hisoka, who betrays the Genei Ryodan in exchange for a chance to fight Kuroro Lucifer. Once Kuroro's powers are "sealed," Hisoka completely loses interest and walks away.
Greed Island Story Arc
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Gon, Killua, and Leorio return to help Kurapika at the end of the third story arc, after which Leorio and Kurapika leave again, returning the focus to Gon and Killua. The fifth story arc concerns Gon and Killua's adventures on Greed Island, the seemingly-magical video game that sucks its player's physical bodies into its own world. It is later revealed that the game is actually set on an island in the real world (the physical game set is actually just a teleporting device), created and run by a group of powerful Nen users who are led by none other than Gon's own father Ging. 'Greed Island' is named after the letters of each name of the creators. The Greed Island story arc is very video-game-like. The game Greed Island runs on a complex card-based gaming system. The goal of the game is to collect a number of set cards, although almost everything in the game, from food to money, can be turned into cards. There are cards capable of doing anything, from making people pregnant regardless of gender, granting wishes, and magic spell cards that can warp you to specific towns. Inside Greed Island Gon and Killua are joined by Biscuit Kruger; nicknamed Bisuke , a 57-year-old woman who looks like a 12-year-old girl, and is a master and experienced teacher of Nen. She continues the Nen training Wing gave to Gon and Killua during the Celestial Tower arc. As the story progresses, a player nicknamed 'Bomber' is bombing other players up, when in fact the there are three. By placing their hand on the person, and saying 'bomber' a bomb is planted there. In order to activate the bomb, they must reveal that they are the bomber, and the bomb will start its count-down. The count-down's speed is according to the pulse of the person. Gon, Killua, and Biscuit team up with other players and take the bombers out. The Genei Ryodan also travel to Greed Island, looking for a Nen remover to remove the dagger placed on Kuroro's heart by Kurapika. Gon, Killua and Biscuit are the first to complete 'Greed Island' and after bidding Biscuit goodbye, they return to their search for Ging. As part of their reward, they are allowed to take three cards to be used in the real world. Using the card 'Accompany' they travel to 'Nigg' who they believe is Ging. 'Nigg' was his father, but his father only wanted Gon to come alone, so he had a safety measure in place, that if "Accompany" was used, it would take them to Kaito instead.
Also during this arc, Killua's little brother, Karuto, joins the Genei Ryodan; replacing Hisoka as member number 4.
Chimera Ant Story Arc
After leaving Greed Island, Gon and Killua meet up with Kaito, the Hunter who told Gon about Ging and Hunters in the very first chapter. They are all hired to investigate a strange insect leg that washed up on a beach. Genetic testing determines that the leg belongs to an abnormally large queen Chimera Ant, an insect that eats other insects and animals, and then gives birth to children that inherit the characteristics of all the different insects and animals it has eaten. The queen Chimera Ant itself just happens to wash up on the shore of an island called the NGL (Neo Green Life) inhabited by a luddite culture, and quickly develops a taste for humans after given the opportunity to eat them. The Chimera Ants proceed to wipe most of the population out and spawn hundreds of offspring before Gon, Killua, and Kaito arrive. The three very powerful Royal Guards are introduced, who develop Nen abilities. One of the Royal Guards, Nefelpitou, fights Kaito and kills him. Kaito is later brought back by Nefelpitou as a puppet used to train Chimera Ants, but his zombification renders him unable to recognize Gon and Killua.
Chairman Netero, Morau, and Novu arrive as reinforcements. However, they are unable to stop the birth of the Ant King. The queen dies because the King ripped himself out of her womb too early. Many of the ants stop being loyal to the King, proclaiming themselves kings, and two even join the Hunters side.
As a side story to the main plotline centered around Gon and Killua, one of the children of the queen Chimera Ant, Zazan, starts a colony near Ryuuseigai, the place that is the origin of the Genei Ryodan. Half of the group: Phinx, Feitan, Shalnark, Shizuku, Bonorenofu and Karuto travel to Ryuuseigai to halt the invasion. Upon reaching the colony, the team splits up, agreeing that whoever defeats Zazan will be the temporary leader of the Genei Ryodan until Kuroro Lucifer's return.
The ants pull a "coup d'etat" on the nearby Republic of East Goruto and from there begin the process of "selecting" humans that have the capability to gain Nen powers. This causes many deaths as only a small amount of humans are able to gain Nen powers.
Currently, Gon, Killua, Morau, Knuckle, Shoot, Novu, and Netero are about to attack the three Royal Guards and the King in the King's palace. However, it has been strongly suggested that something will go wrong with the plan.
The Hunters receive reinforcements from Netero, when he and Zeno appear riding a Nen dragon, which breaks up into countless pieces and provides the necessary distraction for the full assault to begin. Nefelpitou has been temporarily incapacitated after taking the brunt of an attack by Netero. The original plan becomes compromised after Yupi destroyed the stairs supposedly leading to the King. However, the latter is in another building with a seriously injured Gungi girl. He later asks Nef who had arrived to give him a hand against the two assassins to heal Komugi while he will be fighting Netero and Zeno. Both of the assassins and Nef accept the respective requests of Meruem. It is to be noticed that the latter has thus shown his humanity for the first time.
