Following the return of the DigiDestined from the Digital World, Koshiro Izumi discovers a corrupted Digimon on the internet that grows by consuming data. He travels to the home of Taichi Yagami, where they observe its consumption disrupt computer systems across Japan. Taichi and Koshiro are contacted by their Digimon partners Agumon and Tentomon from the Digital World; they battle the corrupted Digimon, but are defeated.

The film focuses on a timid eleventh-grade math genius named Kenji Koiso who has been falsely implicated in the hacking of a virtual world and, with the aid of a classmate's extensive family, must prevent the real and computer-simulated worlds from colliding.