This movie takes place after the Adventure series ends. It begins when a new Digimon Egg is found on the internet, and manages to penetrate into almost every computer system in Japan. When the egg hatches, it's identified as a new kind of Digimon, a Virus-type. It sustains itself by eating data from various system, and starts wreaking havok in Japan. As it consumes more and more data, it continues to evolve. And Taichi and Koushiro decide it's time to stop it. They're off, sending Agumon and Tentomon through the internet to fight off this new enemy. But, with the Virus controlling systems like the American military, all too soon, this digital menace may become all too real. Calling in the help of Yamato and Takeru, they hope that they can stop what's already begun, and maybe save this world a second time. (Source: AniDB)

The gate to the Digital World has been closed for three years. Taichi Yagami and his friends have since moved on, and now that he is in his second year of high school, it is time for him to grow up. While everyone else knows what they want to do with their lives, Taichi remains unsure. Meanwhile, the group drifts further apart as they follow their own paths. One day, a rogue insectoid Digimon called Kuwagamon materializes and disrupts electronics all over the city. Taichi recklessly chases after it and ends up cornered by the attacking Digimon. Suddenly, the Digivice that he still carries—a digital device that serves various purposes including helping one's Digimon partner to evolve—glows, and Agumon appears. The two are able to defeat Kuwagamon, but why did the Digimon cross over to this world in the first place? What is happening in the Digital World, and how exactly does this involve Meiko Mochizuki, the new transfer student in Taichi's class?

Infected Digimon—digital monsters who have begun acting in a berserk manner and experiencing a bizarre increase in power—are invading the real world. While Maki Himekawa and Daigo Nishijima, agents of the mysterious Incorporated Administrative Agency, attempt to learn more about these disruptive appearances, most of the Chosen Children are busy preparing for Tsukishima General High School's summer festival. Mimi Tachikawa, having recently returned to Japan after living in the United States for years, struggles to find her footing among her classmates and fellow Chosen Children. Meanwhile, by throwing himself into his studies, Jou Kido has been deliberately avoiding all issues related to Digimon, causing his partner Gomamon to run away. Mimi and Jou's individual actions cause friction within the group even as the threat of infected Digimon still looms over them. Will the two resolve their personal conflicts in time to help their friends fight off the latest threat?

As the Chosen Children and their partner Digimon live happily together in the human world, Taichi Yagami and Yamato Ishida, alongside their friends, dedicate themselves to maintaining this hard-earned peace. Though united by this innate responsibility, each one has already started to take their first steps toward a future beyond being a Chosen Child. However, this new journey is interrupted by the appearance of Menoa Bellucci, an American professor specializing in Digimon research. She bears news of several Chosen Children from around the world being found comatose, with their partner Digimon nowhere to be found. Menoa's investigations indicate that a new breed of Digimon is behind the alarming phenomenon: Eosmon, who hides within the internet's depths. To succeed in this mission, the team must endeavor through the growing distance between them and band together one last time.