"Digimon Ghost Game" is set in a near-future world where hologram technology has advanced significantly, blending the digital and physical realms. The story centers on Hiro Amanokawa, a reserved and curious high school student, who receives a mysterious device called a Digivice from his father, a renowned researcher in digital phenomena. This device allows Hiro to interact with Digimon, digital creatures that inhabit a parallel dimension. Alongside Hiro are his classmates Ruli Tsukiyono, an adventurous and tech-savvy girl, and Kiyoshiro Higashimitarai, a cautious and studious boy. Each of them gains their own Digivice and partners with a unique Digimon: Hiro partners with Gammamon, a small but energetic dinosaur-like Digimon; Ruli with Angoramon, a calm and wise rabbit-like Digimon; and Kiyoshiro with Jellymon, a mischievous and confident jellyfish-like Digimon.

The narrative unfolds as the trio encounters various Digimon that cross into the human world, often causing mysterious and sometimes dangerous phenomena. These incidents, referred to as "Hologram Ghosts," blur the line between reality and the digital realm, leading to eerie and supernatural occurrences. Hiro, Ruli, and Kiyoshiro work together with their Digimon partners to investigate and resolve these disturbances, uncovering the truth behind the Digimon's appearances and their connection to the human world. The series explores themes of coexistence between humans and Digimon, as well as the consequences of technological advancement.

Throughout the series, the characters face challenges that test their courage, teamwork, and understanding of the digital world. Gammamon, Angoramon, and Jellymon evolve into stronger forms to combat threats, showcasing the dynamic bond between humans and Digimon. The story also delves into Hiro's quest to uncover the truth about his father's disappearance and the broader implications of the Digimon's presence in the human world. As the series progresses, the stakes escalate, revealing deeper mysteries and larger threats that challenge the protagonists' resolve and their ability to protect both worlds.