Gon Freecss grew up on Whale Island under the care of his aunt Mito after his father, Ging Freecss, legally relinquished custody. Initially believing his parents died in an accident, Gon learned the truth at age nine when Kite, Ging's student, arrived. Kite revealed Ging was alive and a Hunter, inspiring Gon to pursue a Hunter License to understand his father. This encounter also showcased Gon's strong affinity for animals, as he protected a Foxbear cub from Kite and later raised it as Kon.

Gon left Whale Island to face the Hunter Examination. Aboard the exam ship, he displayed exceptional physical resilience and sensory abilities, predicting a storm that thinned the candidates. He formed bonds with fellow examinees Leorio Paradinight and Kurapika after aiding an incapacitated candidate, Katzo. The ship's captain, seeing parallels to Ging, allowed Gon to advance after questioning his motives. Gon later befriended Killua Zoldyck, a crucial relationship throughout his journey.

Gon's personality blends cheerful optimism with moral contradictions. Typically friendly and open-minded, he forms attachments based on personal benefit rather than conventional ethics. He expressed gratitude to the serial killer Binolt for training help and admired Hisoka's strength despite his violence. Conversely, he condemned the Phantom Troupe for selective empathy toward comrades while harming innocents, highlighting inconsistent standards rooted in a childlike worldview where "good" aligned with his preferences and "bad" with his dislikes. He also showed intellectual limitations, particularly with mathematics, often causing comedic frustration.

An Enhancer-type Nen user, Gon specialized in augmenting physical capabilities. He developed the signature technique Jajanken, modeled after rock-paper-scissors: "Rock" amplified striking power, "Scissors" transmuted aura into blades, and "Paper" emitted projectile energy. Training under mentors Wing and Biscuit Krueger refined these abilities. Gon possessed heightened senses, including acute smell and vision, and exceptional pain tolerance, fighting on after severe injuries like losing limbs. His latent potential drew attention from formidable figures like Hisoka and Biscuit.

Gon's moral framework fractured during the Chimera Ant arc following Kite's death by Neferpitou. Consumed by vengeance, he acted ruthlessly, threatening the injured Komugi to coerce Pitou into reviving Kite. Learning Kite was irreversibly dead, Gon enacted a Nen contract, sacrificing his future potential and life force for temporary power. This transformed him into an adult-state capable of overwhelming Pitou but left him comatose and near death. Killua later facilitated his recovery using his sister Alluka's wish-granting ability, resulting in Gon permanently losing his Nen abilities.

After recovery, Gon reunited with Ging during the Hunter Association chairman election. Their meeting atop the World Tree unveiled Ging's motivations as an adventurer, letting Gon reconcile his quest's purpose. He acknowledged naivete regarding Kite's death, apologized to Killua for prior hostility, and returned to Whale Island. While Ging suggested Gon might relearn Nen, subsequent manga arcs shifted focus away from him, leaving his training status unresolved. Future narratives may involve Gyro, a reincarnated Chimera Ant with a vendetta against humanity, whom Gon is fated to encounter.

Animated films depict Gon aiding Kurapika in recovering stolen eyes and defending an arena, supplementing his core journey.