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?