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.
To ensure that Netero's last wish will be followed, Ging convinces the other members of the Zodiacs to procede with the election according to some rules defined by him. However, after the first round of voting, a winner is not decided and a second round begins. Meanwhile, Illumi informs Hisoka about Gon's condition and asks for his help to ensure Killua's safety as well, in a plan that somehow involves a fifth, yet unrevealed member of the Zoldyck siblings.
With the elections in a stalemate, Pariston, the current vice-president proposes a new set of rules to his fellow Zodiacs in order to solve the impasse, but the others know that he actually plans to make use of this to secure a victory for himself. Meanwhile, Killua returns home and asks his father to let him see his younger sister Alluka, intending to use her mysterious and frightening power to grant wishes in order to save Gon's life.
Killua reunites with his sister Alluka and uses her as a leverage for them to be allowed to leave the Zoldick state, as her powers can only be used to heal Gon if she is close to him. Meanwhile, Illumi asks for Hisoka's help to stop Killua's plans, and with elections yet to reach a conclusion, the Zodiacs keep arguing about a possible way to bring it to end.
Killua is allowed by his family to leave the Zoldick estate with his sister, but only under supervision of several butlers with orders to bring them home if he ever leaves Alluka's side or allows any of their secrets to be leaked. Meanwhile, Leorio appears and confronts Ging, asking him why he had not ever paid a visit to Gon at the hospital yet.
Leorio's confrontation with Ging earns him the respect of his fellow Hunters and make him one of the frontrunners for the election. Meanwhile, Illumi begins an attack on Killua as part of his plan to kill Alluka, assisted by Hisoka, who has other plans for her.
Gotoh is killed by Hisoka, while the other butlers keep following Killua until he manages to shake them off. Meanwhile, Illumi uses his needles to take control of several people to assist on his plans and when news of it come to the Association, a team of Hunters is assembled to bring him to justice, while some of them decide to take advantage of it in order to win the election.
The election proceeds without a winner determined yet, and Killua is cornered by Illumi, who demands him to reveal which secrets he is hiding regarding Alluka's powers. Meanwhile, Hisoka keeps murdering other hunters just to amuse himself.
With only four candidates left, the election draws to its conclusion and has an unexpected turn when Leorio receives the support from two of the other remaining contestants, who are eager to prevent Pariston from winning. Meanwhile, Killua and Alluka finally arrive at the hospital where Gon is being treated.
Leorio is about to win the election, but loses all motivation to continue after a fully healed Gon appears before him, thanks to the power of Alluka, opening the way to Pariston's victory. Surrounded by his friends and the other hunters who celebrate his recovery, Gon meets his father at last.
Gon apologizes to Ging for failing to save Kite and his father instructs him to apologize to Kite himself instead, affirming that he will wait for him to return. Meanwhile, Pariston wins the election, but renounces in favor of fellow Zodiac Cheadle and Killua seals Alluka's powers away to ensure that he can live a normal life beside him.
Gon apologizes to Kite for not being strong enough to save him. Kite tells him they'll always be friends and that he should go get to know his dad. Gon returns to the Election Hall only to find a note that Ging has gone to the World Tree. Gon, Killua, and Alluka journey to the World Tree where Killua reveals Alluka's powers to Gon. Killua vows to protect his sister and says farewell to Gon, promising they'll meet again. Gon in turn promises to introduce Killua to Ging when they meet again.
Gon climbs to the top of the World Tree where Ging is expecting him, and the two finally have a heart to heart. In this occasion, Ging reveals his intentions to explore the world beyond the current boundaries known to mankind and Gon tells him of all his adventures, while his friends keep following their separate ways, each one of them with their own dreams and goals to pursue.