You play as Marcus Damon, a teenage martial artist and new recruit of DATS (Digital Accident Tactics Squad)—an organization responsible for managing Digimon incidents in the real world. Alongside his partner Digimon Agumon, Marcus is joined by fellow DATS members Thomas Norstein (with Gaomon) and Yoshino Fujieda (with Lalamon). Later, a wild child named Keenan Crier, partnered with Falcomon, also joins the group.

The team’s mission is to investigate strange occurrences involving Digimon appearing in the real world and a series of mysterious child disappearances. As the story unfolds, it is revealed that the Seven Great Demon Lords, a group of ancient and powerful evil Digimon, are manipulating events from behind the scenes. The player must guide the team through both the real and digital worlds, uncovering the truth, battling enemies, and eventually confronting these dark forces to restore balance.