It’s been six years since that summer adventure when Tai and the rest of the DigiDestined crossed over to the Digital World and nearly three years since the final battle between Kari’s second generation DigiDestined and MaloMyotismon. And, at some point, while the peaceful days went by, the gate to the Digital World mysteriously closed. With the gate closed, the days continue to pass, until the adventure "digivolves" once again.
Tai, now in high school, feels downhearted that he and his friends seem to be slowly drifting apart. Meanwhile, strange occurrences are causing electronic devices to malfunction across Odaiba.
Minutes before Tai is due to play a soccer match, a Kuwagamon that had been causing the malfunctions suddenly appears, soon taking physical form and causing collateral damage to the city. Just as Tai is cornered, his Digivice shines and his old partner Agumon appears while digivolving into Greymon to fight the stronger Kuwagamon. As the two Digimon end up traveling through portals to an airport in Haneda, Tai is given a ride by his substitute teacher, Daigo Nishijima. As more Kuwagamon appear, Tai is joined by the other DigiDestined and their Digimon partners, who defeat two of them before a mysterious hand abducts the last one.
Following the battle, as the DigiDestined look over the strange occurrences leading up to Kuwagamon's appearance, which are believed to be caused by distortions in space, Tai and Matt pay a visit to Nishijima, who reveals himself to be part of an organization monitoring Digimon activity, particularly infected Digimon like the Kuwagamon that appeared. As Izzy develops ways to provide easier access to their Digimon partners and seek out digital disturbances, Tai begins to fear that people could get hurt as a result of his actions as a DigiDestined.
The next day, a mysterious black Digimon known as Alphamon appears, seemingly targeting a Digimon under the care of Meiko Mochizuki, a girl who recently transferred into Tai's class. With Alphamon proving too powerful for the other Digimon, Matt urges Tai to stop running away from his fears, and together they manage to drive Alphamon off with the power of Omnimon. Afterwards, Meiko reveals that she is also a DigiDestined with her partner, Meicoomon, being the Digimon that Alphamon was targeting.