While one of the examinees, wrestler Todo, criticizes Menchi and all Gourmet Hunters, Netero, the head examiner and Hunter Association's president, arrives and asks Menchi to give everyone another chance. The test takers collect spider eagle eggs, and Todo learns to respect Gourmet Hunters, vowing to return and take the test again.

Gon, Kurapika, and Leorio reach the first stage of the Hunter Exam, a seemingly endless forced run through a tunnel leading by the examiner named Satotz. They are befriended by Tonpa, a man taking the exam for the 35th time, and meet Killua, another entrant. In the end Tonpa betrays Leorio, as Gon and Kurapika go looking for them.

The group starts stage 2 of the test, which is to satisfy Gourmet Hunters Buhara and Menchi with their cooking. Everyone satisfies Buhara's taste for BBQ pork, but they all fail to make sushi good enough for Menchi. She says all examinees fail.

The successful examinees are taken by blimp to an island hotel. In order to pay for the rooms, they dive to collect treasure from sunken ships. Kurapika explains to Leorio that everyone from his clan was killed by the Phantom Troupe for their eyes. When a member of the Kurta clan dies with their emotions ablaze, their Eyes become Scarlet and are treated as treasures.

The hotel owners leave the examinees stranded on the island. A map is found indicating another island nearby, and part of the group sets out immediately to find it, dying when a storm hits. Hanzo and Kurapika sense danger and are elected leaders of the people who stay. They learn of a storm that comes in daily waves, the second of which will submerge the island, so they have one day to escape.

The protagonists and others have passed the second stage, and they fly towards the next stage on a blimp. Anita, a girl who failed the earlier test, sneaks aboard to get revenge on Killua for the death of her father. The Hunters capture her, and Chairman Netero offers to free her if Gon and Killua can take a ball from him.

Several days pass as Gon recovers from being poisoned. Killua is stalked by Imori, one of Amori Brothers. Imori's brothers Umori and Amori show up, and Killua bests them and gets his number badge from Amori. All the protagonists now have their points except for Leorio, who goes looking for his target Ponzu. He finds her in a cave, but is poisoned by snakes. Gon and Kurapika go inside to help him.

Gon Freecss runs into a Foxbear in the forest. A mysterious stranger named Kite saves Gon by killing the beast. This man tells him that his father Ging is alive. Gon decides to take the Hunter Exam and become a professional Hunter, but can only do this after catching the Master of the Swamp to convince his Aunt Mito to let him do it. Despite her feelings, after Gon catches it, Mito allows him to begin his adventure.

Gon's aunt Mito gives him the go ahead to take the Hunter Exam after he has successfully passed her test, using a special rod from his father. Gon goes to town to catch a ship to the exam. In town, Gon befriends Leorio, after several run-ins with each other through the town. Leorio is also intent on taking the exam, and they take down a cruel animal show. In the end, they almost miss the ship, but through Gon's quick thinking, they manage to board the ship at the last minute.

On the ship to the exam, Gon and Leorio meet Kurapika. The captain asks each for their reason to be a Hunter. Gon wants to find his father, Leorio wants to be rich, and Kurapika wants to be a force for justice.

Majitani feigns unconsciousness in an attempt to run out the clock. Leorio and the leader of the prisoners bet on whether he's faking. Leorio holds the man above a long drop, and Majitani wakes up. He concedes the match to Kurapika, but the group loses a large chunk of their time because of the bet.

Leorio goes next. His opponent is Leroute, an attractive woman. He loses ten hours in bet to her so that he can grope her. He then loses the rest of their betting hours to her in a game of rock, paper, scissors. Killua then faces Johness the Dissector, a serial killer responsible for the murder of at least 146 people with his bare hands. Killua rips out his heart, explaining afterwards that Johness is an amateur and he is a pro.

The fourth stage of the Hunter Exam is a manhunt on Zevil Island. Each examinee must collect 6 points; their own number badge is worth 3, the number badge of their target is worth 3, and any other number badges are worth one point. Gon's target is Hisoka, and he practices catching birds with his fishing pole to prepare. He realizes he must attack Hisoka when Hisoka attacks his own target. Gon learns this by watching birds catch fish from the water.

Gon, Leorio and Kurapika become trapped in the cave with Ponzu. Leorio has been poisoned, and Gon gets bit numerous times to retrieve the antidote. Gon uses Ponzu's sleeping gas to put the snakes to sleep while holding his breath and rescuing everyone. Leorio takes Ponzu's number badge while she sleeps and Gon retrieves the number badges given to him by Hisoka, reasoning that it's OK to use them so that he can remain with his friends. The fourth stage ends.

Gon is determined that Killua has left against his will and Gon is going to find him. He fights Illumi for information and Illumi is about to kill him when Hisoka shows up. Illumi instead tells Gon that Killua is at the Zoldyck family home. Leorio is about to go to medical school and Kurapika is about to leave on his first job when both change their minds and decide to follow Gon as he looks for Killua.

Killua stops trying to take the ball from Netero because his killer instincts are surfacing. Anita escapes her handlers and attacks Killua, who comes close to killing Anita, but lets her live because otherwise Gon would get mad at him. Gon is never able to get the ball, but makes Netero use his left leg and both hands once, and is satisfied.

The objective of stage 3 is to get down from a tower alive. The group is forced to team up with Tonpa, and their test is to win 3 out of 5 matches against tower prisoners. Tonpa takes the first match with a hardened-looking criminal, and promptly gives up. He explains that he doesn't want to be a Hunter, he just likes watching others fail and be killed.

Gon faces the next prisoner, Sedokan, in a match to see who's candle can burn the longest. Gon is given a candle that burns quickly, but because of this it isn't susceptible to the wind, and Gon drops it on the floor and runs to blow out Sedokan candle. Kurapika engages in a death match with the next opponent, Majitani, but refuses to kill him after seeing red (literally) and knocking the criminal unconscious.

The group works together to separate the battleship/hotel from the island before the second wave of the storm hits. Leorio gets stuck on the bottom of the ocean in a diving suit and Gon helps him escape. Gon is then saved by Hisoka. Kurapika is knocked out but the steering is done by a mysterious examinee who seems to be Hisoka's ally. They separate the ship just in time, and a blimp comes to pick them up.

Gon, Kurapika and Leorio continue on the test, arriving at a cabin in the woods. A husband and wife say they have been attacked by beasts, when a beast shows up and kidnaps the wife. Leorio stays to treat the husband's wounds as Gon and Kurapika help the wife. In the end it turns out the couple and the beasts are a family and they find the group worthy of continuing to the next test.

Tonpa has placed Leorio and another examinee near hallucinogenic sap. In a dream state, he explains that he wants to be a Hunter to get money so he can become a doctor who doesn't charge for his services. Gon and Killua bond. At the end of the first stage, a man appears to accuse the examiner of being a fake.

Chairman Netero interviews the nine remaining examinees (Gon, Kurapika, Leorio, Hisoka, Hanzo, Pokkle, Gittarackur, Bodoro, and Killua) in preparation for the final test. He asks each who they are interested in, and who would they least like to fight out of the nine. He then unveils a brackets system for the upcoming tournament between the remaining examinees.

Hisoka and Kurapika fight in the first fight of the final stage. Hisoka toys with Kurapika at the beginning, but when Kurapika becomes angry they are on similar levels. This causes Hisoka to force himself to calm down. He then whispers something to Kurapika and declares himself the loser of the match. Kurapika is now a Hunter.

The next fight is between Hanzo and Gon. Although Gon tries his hardest to combat Hanzo, it is obvious he is no match for the ninja. Hanzo severely injures Gon and breaks his arm, but Gon will not admit defeat. Gon feels that if he is ever to find his father, he must pass the Hunter Exam now.

Gon, Leorio and Kurapika take a train towards Killua's home on Kukuroo Mountain. The last leg of the trip is spent on a tour bus that takes them to the Door to Hades, a giant gate that hides the path to the estate. A beast named Mike waits behind the gate, so Gon asks the security guard, Zebro to call Killua and have him open it from the inside.