Twelve years prior to the start of the story, Ging Freecss left his infant son, Gon, with Gon's aunt Mito on Whale Island. Gon, raised believing both his parents were dead, finds out from Ging's apprentice, Kite, that his father is still alive and has since become an accomplished "Hunter". Hunters are licensed, elite members of humanity who are capable of tracking down secret treasure, rare beasts, or even other individuals. Gon leaves his home to follow in his father's footsteps as a Hunter by taking the "Hunter Examination", a series of brutal tests involving skill, survival, and teamwork. Prior to and during the exam, Gon meets and befriends three of the other applicants: Kurapika, the last remaining member of the Kurta clan who wishes to become a Hunter in order to avenge his slain people; Leorio, a prospective physician who claims to desire to become rich; and Killua Zoldyck, who fled his life as a member of a notorious assassin family. Among many other examinees, Gon continuously encounters Hisoka, a deadly and sadistic magician. After the exam and a brief excursion to Killua's home estate, the four protagonists split up, promising to meet up in a place called Yorknew City months later. Kurapika departs to find work and Leorio leaves to attend medical school. Gon and Killua decide to gain both combat experience and money at the "Heavens Arena", a skyscraper where thousands of martial artists compete daily in fighting tournaments. There they meet a kung fu master named Wing, who trains them in utilizing "Nen", a chi-like life energy that can be used to manifest superhuman powers.
The next story arc reunites the main characters for the world's largest auction in the sprawling metropolis Yorknew City. Gon, Killua, and Leorio try different methods to make enough money to buy "Greed Island", an extremely rare and expensive video game with Nen-like properties that may help Gon locate his father. Meanwhile, Kurapica, having mastered a form of Nen himself, takes a job as bodyguard for a rich client who is attempting to obtain a pair of Kurta eyes. While in at the auction, Kurapica crosses paths with the Phantom Troupe, also known as the "Spiders", a criminal group attempting to steal valuable artifacts throughout the city's many auctions. The group is led by its founder Kuroro Lucilfer, a powerful Hunter capable of stealing others' Nen abilities and the leader of the group responsible for the slaughtering of the Kurta clan (Kurapika's people). With the help of his comrades, Kurapica forces Kuroro out of the Phantom Troup and halts the group's activity in Yorknew City. Finally, Gon and Killua find Greed Island, the seemingly-magical video game that sucks players within. 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. Inside Greed Island Gon and Killua are joined by Biscuit Krueger, a master and experienced teacher of Nen who trains them. With the help of many other players, Gon and Killua clear the game. As part of their reward, they are allowed to take three cards to be used outside the game. Using one of the cards, Gon and Killua travel to the location of a player with the username "Nigg", who they believe to be Ging. However, it ends up bringing them to Kite instead.
Alongside Kite, Gon and Killua briefly work as biological researchers in the country of Kakin. As they investigate a giant insect limb found on the country's shores, the group discover it came from a man-sized Chimera Ant queen, an insect that devours other creatures and then gives birth to progeny that inherit the characteristics of the different species it has eaten. The queen washes up onto island nation called the Neo-Green Life (N.G.L.) Autonomous Region, inhabited by a neo-luddite culture. She quickly develops a taste for humans and builds a colony in order to conceive both an army of offspring and a Chimera Ant king named Meryem. The Chimera Ants proceed to wipe most of the population out before Gon, Killua, and Kite arrive. The queen dies during labor, and the king and his Royal Guards flee the N.G.L., secretly overthrowing the government of the nearby Republic of East Gorteau soon thereafter. Under the guise of the former king of the Republic, Meryem initiates the process of forcibly awakening Nen in the civilians of East Gorteau in order to form his own personal army to conquer the world, resulting in the deaths of millions unable to awaken Nen. As Ants formerly under the queen's rule rejoin the king, the Hunter Association mobilizes quickly to stop the oncoming genocide by sending in an extermination team of Hunters to East Gorteau. Distraught over the murder of Kite at the hands of the Royal Guards, Gon and Killua join the extermination team in order to take revenge for their friend.