To Meiko Mochizuki's dismay, her Digimon companion Meicoomon is compelled to transform into Meicrackmon, succumbing to a sinister influence during the change. When Meicrackmon vanishes to unleash chaos elsewhere, it appears that the Digital World itself begins to reject Meiko and the other Chosen Children. While dodging numerous foes that pursue them, the party strives to chart a path back home. Their journey is fraught with peril, as unseen threats loom at every turn.
In the human realm, an envoy from the enigmatic force Homeostasis approaches both Meiko's father and Daigo Nishijima of the Incorporated Administrative Agency to talk about Meicoomon's origins. The envoy tells them that Homeostasis intends to destroy the digital beast, aiming to stop more Digimon from appearing in the human world—no matter how the Chosen Children feel about it.