The Chosen Children are in shock after the betrayal of Meicoomon, the digital monster who had recently joined their group alongside her human partner, Meiko Mochizuki. Koushirou Izumi is determined to diagnose the infection that took control of Meicoomon. Meanwhile, Takeru Takaishi realizes that his own partner, Patamon, is starting to exhibit alarming symptoms similar to those of other infected Digimon, like Meicoomon. Just then, the Chosen Children receive a message from the mysterious entity Homeostasis, who informs them that their world is in danger of total destruction—and the Digital World, the home of the Digimon, is too. Homeostasis plans to enact a "Reboot," which will reset all the data that makes up the Digital World and eradicate the infection. However, the Reboot will also erase the memories of all Digimon, including the Children's partners. Can the Chosen Children stop Meicoomon before the Reboot becomes necessary, or is this the end of their time together with their Digimon?

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?

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?

The five digi-destined children stumble upon an ancient island inhabited by two different types of digimon; The Beast types, and the Human types. When they see two young digimon-a beast and humanoid-have become friends, they decide something must be done about the feud. (Source: ANN)