Ten thousand years ago, a great and powerful Digimon was defeated and sealed away by the Holy Knights as the "Digi Core". Years later, a virus infected the digital world, leaving only those that possessed the D-Antibody (X-Antibody) remaining. The only members of the Holy Knights remaining are Omega of Power (Omnimon X), Duke of Courage (MedievalGallantmon/Gallantmon X), and Magna of Miracles (Magnamon).

At the start of the series, the "God of Death" MetalPhantomon draws Hikaru, Kiyoshi, Masuken, and Teru into the digital world. Originally, Hikaru is left alone with his Digimon (which starts out as a Dorimon), and has to battle his friends Teru and Masuken, who are under MetalPhantomon's control.

At one point, MetalPhantomon steals the "Dragon Spirit" of Masaru's partner, who is now a Dorumon. While MetalPhantomon uses it to revive the Digi-Core, Hikaru, Teru, and Masuken learn from Omega of Power that they can get a new Dragon Spirit from Duke of Courage - with this, they can save Dorumon's life. But when they arrive in Duke's area of the Digital World, they are given a series of tests by Duke's servant, MameTyramon.

After completing the tests and battling Duke himself, they manage to earn Dorumon a new Dragon Spirit. However, now they must battle MetalPhantomon, who has resurrected the Digi-Core as Dexmon. In the end, Hikaru and the others manage to save their friend Kiyoshi, who was sealed inside Dexmon, and return to the real world.