Mikey Kudo, a 7th grade boy, heard a mysterious melody and followed it to an alley where a mysterious, legendary Digivice called the Fusion Loader appeared in front of him. Accompanied by his friends, Angie Hinomoto and Jeremy Tsurugi, they were dragged into the Digital World. They soon realized that the Digital World was a place inhabited by living creatures named Digimon and is now slowly being taken over by an evil empire named the Bagra Army. Now, Mikey and his "Fusion Fighters" team become an important figure to free the world from the Bagra Army, led by their Emperor Lord Bagra.
Mikey and Shoutmon return to the Digital World and find that it has been taken over by the evil Bagra Empire and is ruled by seven Dark Generals.
The Dark General prepares to delete the rest of the Fusion Fighters; Christopher and Metal Greymon help Mikey and Shoutmon on a rescue mission.
The Blue Flare and the Fusion Fighters head to Vampire Land; a group of helpless Digimon are kidnapped by NeoMyotismon.
When Metal Greymon is absorbed by NeoMyotismon, Mikey and Shoutmon search for the legendary White Lopmon to help.
The Fusion Fighters travel to Honeyland where innocent Digimon are being drained of their energy.
The Dark General of Honeyland invites Mikey and the Fusion Fighters to a day of horrors in his own personal theme park.
Nene's search for her little brother finally comes to an end, but she is devastated to learn that Ewan is a general for Lord Bagra.
As the team enters Cyber Land, they discover a friendly girl who is eager to join their team; Dorulumon is suspicious of Luca's intentions.
The shape-shifting Dark General of Cyber Land works to break up Mikey, Shoutmon and their friends with a series of impersonations and traps.
Angie becomes concerned when she hears Beastmon talking in her sleep about how the Digital World and the human world are facing a crisis.
Mikey finds and rescues the Digimon known as Spadamon, who explains that the Sweets Zone has been taken over by the Bagra Army's Matadormon.
In the Sweet Zone's underground, Mikey and the gang attempt to search for and save everyone only to find themselves surrounded by Raremon.
Mikey and the gang come to the Sword Zone, where all Digimon hope to become real swordsmen, but Grademon arrives and attacks them.