The Chosen Children have been reunited with their Digimon partners, who no longer remember them due to the effects of a digital reset. While everyone tries to reconnect with their digital monsters, Sora Takenouchi encounters resistance from Piyomon, who stubbornly refuses to speak to her. Suddenly, an attack by a hostile Digimon separates the group, scattering them and their Digimon across the Digital World.

Back in the human world, Daigo Nishijima of the Incorporated Administrative Agency receives a warning that a new entity is in pursuit of "Libra," which he believes to be an alias for Meicoomon. For some reason, Meicoomon retains all of her memories and therefore still recalls her partner Meiko Mochizuki, who has come alone to the Digital World to find her. If they hope to identify what other forces have been driving the incidents thus far, the Chosen Children must survive the obstacles of the recreated Digital World and make their way back home.