While preparing for the upcoming school camp, Taichi Yagami is visited by his new neighbor Koshiro Izumi when they learn that Tokyo’s electronic systems have gone haywire, including the city's trains with Taichi's younger sister Hikari and their mother trapped in one. The two youths run to the nearby station where Taichi is suddenly transported to another world located inside the internet, encountering a wounded Digimon called Koromon. Upon making contact with Koromon, Taichi gains a Digivice while Koromon evolves into Agumon. Koshiro, who also obtained his own Digivice, contacts Taichi and informs him that a horde of Digimon called Argomon are responsible for the chaos with Taichi and Agumon battling them to save the former’s family. Though the remaining Argomon evolves into more powerful forms before overpowering them, Taichi and Agumon’s determination triggers the latter’s evolution into Greymon.

The battle between Greymon and Orgemon ended abruptly and now the Chosen Ones discuss their next move. Taichi and Agumon take a chance to defeat the ultimate enemy, so that the others can safely head to their next destination.

The six Chosen Ones who had finally gathered split up again into two teams in order to find the Holy Digimon. As Yamato’s team attempts to cross the desert, they encounter some dust devils.

The Chosen Ones worked together and succeeded in defeating Ultimate Digimon Orochimon. However, a mysterious countdown begins. To save Tokyo, they must prevent it from reaching zero

Yamato’s younger brother, Takeru, is unexpectedly found in the Digital World, held captive by a powerful Digimon. With the help of Leomon’s army, Taichi and Yamato attempt to save Takeru.

Taichi’s younger sister Hikari and Koshiro's group are brought to the Digital World just in time to save Taichi's group. The Chosen Ones are now reunited once again. However, another disaster, this time at a rocket launch site, hits the real world.

The Chosen Ones come to face their old enemy, Darkknightmon. Patamon evolves into Angemon again to fight off Darkknightmon. However, the children are all separated and sent to different parts of the continent.

Taichi and Agumon finally surpassed their limit, and Agumon evolves into Wargreymon. This evolution awakens Lopmon’s long-lost memories. And Taichi learns about the new threat, Millenniumon.

Taichi’s party finally catches sight of Skullknightmon and Hikari, who was kidnapped. Taichi chases after them, but Hikari is swallowed into the darkness.