The story focuses on a young boy named Gon Freecss who discovers that his father, who left him at a young age, is actually a world-renowned Hunter, a licensed professional who specializes in fantastical pursuits such as locating rare or unidentified animal species, treasure hunting, surveying unexplored enclaves, or hunting down lawless individuals.

Hunters (ハンター, Hantā) are licensed, elite members of humanity who are capable of tracking down secret treasures, rare beasts, or even other individuals, and can also access locations that regulars cannot.

[11][12][13] 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 clan and recover their scarlet-glowing eyes that were plucked from their corpses by a band of thieves known as the Phantom Troupe; Leorio, a prospective physician who, in order to pay for medical school, desires the financial benefits that Hunters receive; and Killua Zoldyck, another twelve-year-old boy who has left his former life as a member of the world's most notorious assassin family.

After many trials together, Gon and his friends end up passing the exam except for Killua, who fails after killing another applicant due to the influence of his brother, Illumi, and runs away to his family's estate in shame.

After Gon and the others convince Killua to rejoin their side, Leorio and Kurapika depart temporarily for their own personal reasons, while Gon and Killua set for the Heavens Arena (天空闘技場, Tenkū Tōgijō), a skyscraper where thousands of martial artists compete daily in fighting tournaments, seeking to improve themselves and gain monetary rewards.

[14] There they meet Zushi, a fellow Heavens Arena applicant, who has a kung fu master named Wing who trains them in utilizing Nen, a Qi-like life energy used by its practitioners to manifest parapsychological abilities, and is also considered to be the final requirement to pass the Hunter Exam.

During the occasion, two from the band of thieves are killed by Kurapika and he is forced to give up the chance of hunting down the rest in order to rescue Gon and Killua from being captured, but not without succeeding in sealing the powers of their leader, Chrollo Lucilfer.

A few days later, Gon and Killua achieve their objective and begin playing Greed Island, an extremely rare and expensive video game with Nen-like properties following some clues about Ging's whereabouts.

They decide to help with Kite's research of 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.

Upon facing the Royal Guard of the Chimera Ants, Kite sacrifices himself to allow Gon and Killua to flee and alert the Hunter Association.

After the Chimera Ant incident is resolved, the Hunter Association's top echelons the Zodiacs, from which Ging is a member, begin the process of choosing Netero's replacement as Chairman, while Killua returns home to ask for his younger sister Alluka to save Gon's life.

Some time later, Netero's son Beyond assembles an expedition to the Dark Continent (暗黒大陸, Ankoku Tairiku), the forbidden, vast area outside of the known world; he is sponsored by the Kingdom of Kakin.

Fearing that the expedition may bring disaster, just like in all previous attempts, the world's five greatest powers accept that Kakin join their ranks in exchange for full authority over its findings.

To accompany Beyond and ensure his compliance, the Zodiacs decide to watch over him and invite Kurapika and Leorio to join them, replacing Ging and former Vice-Chairman Pariston Hill, who assembled their own Dark Continent exploration teams by Beyond's request.

After reviving through Nen, Hisoka starts killing off the Phantom Troupe members one by one, who have boarded Kakin's ship to the Dark Continent to rob it.

Kurapika's personal objective, however, is to retrieve the last batch of scarlet eyes of the Kurta Clan in custody of Tserriednich, Kakin's Fourth Prince.

[21][22] With the birth of their first son early in its publication, Togashi felt that this personal aspect of his life would be a great influence on his work, particularly the manga's theme of a young boy searching for his father.

[19] There have been several instances in which Togashi has apologized to readers in Shueisha's Weekly Shōnen Jump for low-quality artwork and promised to redraw portions of the chapters for their tankōbon (collected volume) releases.

[48][49] On October 1 of the same year, Togashi made his first tweet in nearly seven months, which contained the phrase "Start over" in English, as well as an image depicting the bottom right corner of a page with a ruler below.

[64] The series has also been published in a sōshūhen edition that aims to recreate the manga as it was originally serialized in Weekly Shōnen Jump in the same size and with the color pages.

The series is directed by Hiroshi Kōjina, produced by Madhouse, scripted by Atsushi Maekawa, and character designs were created by Takahiro Yoshimatsu.

[110] Produced by Studio Pierrot and directed by Noriyuki Abe, it depicts the early events of the manga up to Gon's ocean voyage from Whale Island.

[177][178] In North America, volumes 23 through 27 have ranked within the top 300 best-selling graphics novels list of sales estimates by Diamond Comic Distributors.

In his 2007 book Manga: The Complete Guide, Jason Thompson described its storyline as "an almost random collection of psych-outs, battles, puzzles, and trickery" that works on both a chapter-by-chapter basis and a larger scale.

Thompson did note how the artwork during its magazine run is often "sketchy" and missing backgrounds, but that Togashi goes back and fixes it for its collected tankōbon release.

[185][186] Publishers Weekly gave a positive review to the first volume of the manga, stating that Togashi "shows a deft touch" with its standard story, calling his artwork "clear and graceful", and mentioning that his characters are "endearing and complex".

[5] Beginning with the second Viz DVD volume, Kimlinger summarized, "Togashi's plotting is canny and occasionally insightful and Furuhashi's visuals inventive yet attuned to the measured pacing of the series.

"[77] Tucker admitted to being "bewitched" by the series mainly due to the remarkable and original characters, especially the interplay between the vastly different personalities of the Phantom Troupe members.

"The artistry not only shows its age but, in fact, looks older than it actually is," the reviewer commented, "hearkening back to a day when digital coloring and CG enhancements were not ubiquitous and allowances for a rougher look were greater."

"[196] According to Movie News Guide and Latin Post, the Madhouse's 2011 version received more viewers not only in Japan but also around the world, particularly in North America.