Masaru Daimon conoce a Agumon, un Digimon perseguido por la agencia DATS. Cuando se hacen compañeros, se unirán a Tohma y Yoshino.

The Digital Accident Tactics Squad (DATS) is a government organization that consists members for the team, including Marcus Damon, Agumon, Thomas H. Norstein, Gaomon, Yoshino "Yoshi" Fujieda, Lalamon, Keenan Crier and Falcomon. The organization sends any Digimon back to the Digital World.

Marcus learns that Merukimon is opposing mankind. However, the past is revealed that scientist Akihiro Kurata was responsible for invading the Digital World. Kurata gained the support of the government about opposing all Digimon species, claiming they were a threat to mankind. Kurata frees and awakens Belphemon, one of the Seven Great Demon Lords. When he merges with him, Marcus defeats them. Before dying, Kurata uses a bomb to make the Digital World merging with the human world. While BanchoLeomon prevents the collision, he asks Marcus to stop King Drasil (Yggdrasil), the supreme ruler who attempts to protect the Digital World by destroying mankind, since they cannot exist in both dimensions. Marcus realizes that his father, Spencer, was trapped in the Digital World for ten years, because Drasil possessed Spencer's body and BanchoLeomon kept the latter's soul. After Marcus destroys Drasil, Spencer's soul returns to his body.

With both worlds restored, all Digimon partners return to their own world. Five years later, Marcus and his friends embrace their future.

大门大意外地遇到了亚古兽，两人见面就大打出手，亚古兽战败后称大门大为大哥，但是数码特搜部队（DATS）不容许未受其队员管理的数码兽留存在这个世界上，必需送回数码世界，而后汤岛告诉大若加入DATS他就可以跟数码世界的强敌战斗，大因此加入DATS，与淑乃及托玛组成小组，一同解决数码事件。

托玛发现日本的数码事件频率增加并非偶然，因此请假回到欧洲调查，发现根源来自于人类的七宗罪。而比丘兽的事情让大他们知道了其幕后黑手是究极体数码兽——墨丘利兽搞的鬼，也因此决定动身前往数码世界。而在数码世界，他们见到了一个人类小孩——郁人，他自称数码兽，对人类怀有怨恨。

历经艰难以后和汤岛老人会合并见到了墨丘利兽，墨丘利兽指责人类没有遵守约定，严重干扰了数码世界的秩序，对数码兽实施残酷的杀戮，然而汤岛却一再强调人类什么事情都没有做。最后谈判破裂，汤岛一面努力制造混乱局面，一面把大一行人送回了人类世界，自己却留在了数码世界。回到人类世界的大家决定去见见郁人的父母。

在见到郁人的父母后，郁人拒绝承认自己人类的身份，在大的开导下，他才准备融入这个家庭，并希望回到数码世界，跟墨丘利兽告别。然而等待他们的，却是墨丘利兽的死亡，而杀死它的，就是曾经和大的父亲，郁人的父母以及汤岛、萨摩一同前往过数码世界的仓田。最后，大门大为DATS中唯一一位留在数码世界者。