Mikey and Shoutmon return to the Digital World but discover it has been completely taken over by the evil Bagra Empire and divided into seven lands, ruled by seven Dark Generals who all have the power to Digi-fuse.
Christopher and Metal Greymon's strength is put to the test when they join Mikey and Shoutmon on a rescue mission to save the rest of the Fusion Fighters from being deleted at the hands of the Dark General Dorbickmon.
The Fusion Fighters travel to Honeyland, where innocent Digimon are being drained of their energy in order to make digi-honey. They also meet a potential new ally named Mervamon, but her extremely narrow-minded focus on defeating the Dark General and inability to work with the team alienates several of the Fusion Fighters.
Nene's search for her little brother Ewan finally comes to an end, but she is devastated to discover that Ewan is a General for Lord Bagra and her brother thinks the Digital World and Digi-Fusion is just a glorified game with no consequences.
As the team enters Cyber Land, they discover a friendly little girl named Luca who is only too eager to join their team. Only Dorulumon is suspicious of her intentions, but can he prove that Luca is up to no good?
The evil shape-shifting Dark General of Cyber Land continues his work to divide and conquer Mikey, Shoutmon and their friends with a series of impersonations and traps. Can they see through the ruse and work together to stop him?
With Baillistamon's evil form, Dark Volumon, revealed and Nene and Mikey kidnapped by Olegmon, Shoutmon must team up with Christopher and Team Blue Flare to save their friends and return Ballistamon to his true self.
The Fusion Fighters pour their energy into the fight against Dark General Gravimon, who in addition to his fearsome army and ability to re-constitute his body, has set his sights on taking the power of X7 for himself.
While Christopher, Nene and the other Fusion Fighters battle Apollomon Whispered and his evil comrades, it's up to Mikey to convince Ewan that the Digital World isn't a game and that losing has real world consequences.
As the dark side of Apollomon, Apollomon Whispered, grows stronger, Mikey must come to terms with the fact that his ally may be lost to him forever. With a new sense of teamwork and dedication to each other, the Fusion Fighters regroup in order to try and defeat the last Dark General.
With all seven Dark Generals destroyed, the Fusion Fighters finally arrive at Lord Bagra's castle. There, they come face to face with AxeKnightmon and all seven of the Dark Generals, regenerated to fight against them!
In an attempt to save his friends, Mikey allows Axeknightmon to extract his Digi-Core and is sent to the dreaded Holding Cell of Prison Land. There, he comes face to face with the cores of the seven Dark Generals, who are only too happy to band together and defeat the Fusion Fighter General.
After escaping Prison Land, Mikey and the Fusion Fighters finally come face to face with Lord Bagra. But when he personally absorbs the Dark Code Crown, he becomes stronger than they ever could have imagined, and set to take over not only the Digital World but the Human World as well!
After witnessing Axeknightmon's treachery, the Fusion Fighters fear all hope is lost as they battle the newly fused and immensely powerful Darkest Axeknightmon and receive some unexpected help from a pair of old friends.
With both the Human and the Digital Worlds invaded by MegaDarkness Bagramon, the Fusion Fighters have one last hope - the Order of the Knights! With their help, Mikey sets on a desperate mission to save Shoutmon, while both good and evil Digimon clash in one last epic battle for the future of both worlds.