A 14-year-old boy, Marcus Damon, an undefeated ultimate fighter (street fighter in the original Japanese version), meets Agumon, who has escaped from the Digital Accident Tactics Squad (DATS), a secret government organization set up to defend the human world from invading wild Digimon. After fighting each other, the two quickly become friends, and through a series of events, are inducted into DATS, where they hope to grow in strength.
Marcus’ team-mates include the 14-year-old Thomas H. Norstein, a young prodigy, with his partner Gaomon, and 18-year-old Yoshino “Yoshi” Fujieda who has Lalamon for her partner. As the series progresses, Thomas discovers that Digimon respond to the “darkness” in humans, putting them at odds with monsters who seek to use humanity’s own vices to bolster their own power.
The plot thickens with the introduction of Merukimon, one of the rulers (as a member of the Olympus Twelve, Merukimon has deity status in the Digital World), of the Digital World who rules the eastern Digital World and lives in the Infinite Ice Ridge, Biyomon and the human boy Keenan Crier, who serves him along with his partner Falcomon. The DATS team tries to unfold the reason for their hatred of humankind, until it is revealed that the real enemy was Akihiro Kurata, a scientist who led an attack on the Digital World years before that resulted in the death of many Digimon, including Keenan’s adoptive mother, Frigimon.
Kurata gained the support of the Japanese government and important businessmen like Thomas’ father on his plan to destroy all Digimon in the Digital World, claiming they were a threat to mankind. But this was only a facade to occult his main objective. He harnesses the energy of the Digimon he destroyed to power-up Belphemon, one of the Seven Deadly Digimon/Seven Great Demon Lords, and uses it in his attempt to rule the Human World (and eventually the Digital World), but his ambitions were shattered by the efforts of Marcus and his allies. Kurata merges with Belphemon and gets revenge on Marcus for constantly foiling his plans, but Marcus and ShineGreymon managed to defeat Belphemon, thanks to their friendship efforts.