如果说数码暴龙第一部的主题是勇气，第二部的主题是友谊，Tamers的主题是梦想，Frontiers的主题是奇迹，Savers的主题是人性，那么这部剧场版的主题应该是生存。一场离开了人类，数码暴龙独立的生存战争。
The Digital World is becoming so overpopulated that the super computer, Yggdrasil, that governs the Digital World can't handle it anymore. His solution is to wipe out the vast majority of the Digimon with the X Program. He chooses a very small percentage to be moved to a new Digital World because he plans to destroy the old Digital World. Those who were not chosen but survived anyway and moved to the new world had a rare gift known as the X-Antibody, this antibody when activated changed their appearance and made them more powerful. Those who have the X-Antibody are generally distinguished by the X in their name and sometimes an X placed on their body somewhere (for example Tokomon's X on the forehead). There are few with the X-Antibody that are not distinguished by an X after their name but this is because there is no other version of them in existence that doesn't have the X-Antibody so there is no need to distinguish the normal and X-Antibody apart with the X surname. Yggdrasil is protected by the Royal Knights, including Omnimon, Gallantmon and Magnamon, who eliminate X-Antibody Digimon. They are three of the four Royal Knights seen in the Movie the fourth being Alphamon, who is missing.
One of the outcasts is a strange, furry dragon-like Digimon named Dorumon. Dorumon seems to be rejected by everybody, and is attacked by a Leomon who wants his X-Antibody. Leomon eventually dies and asks Dorumon to live for him. WarGreymon X tries to make peace with a group of normal Digimon (consisting of Andromon, Apemon, Blossomon, and Tokomon) and X Digimon (consisting of Garudamon X and Kokuwamon X), but Omnimon shows up and eliminates them all except WarGreymon X and Tokomon who escape. The two crash land at a temple where Dorumon lives. WarGreymon X leaves Tokomon in Dorumon's care and draws Omnimons fire. Omnimon fights them later, seriously wounding Tokomon and Dorumon. MetalGarurumon X and WarGreymon X show up to battle Omnimon. MetalGarurumon X was mortally wounded and apparently dies, but not before giving his X-Antibody to the fatally injured Tokomon. Dorumon, anguished by the sight, digivolves into Dorugamon in response to Omnimon's assault. WarGreymon X draws their fire and just before Omnimon attacks Gallantmon intervenes. Gallantmon believes Yggdrasil's plan to eliminate the X-Digimon and all associated with them is wrong, but when he tried to convince Omnimon of his view, he was impaled by Omnimon's blade. Before his apparent death, Gallantmon mentions to Omnimon that there is something he needs to check. He then dissolves into data and seemingly dies. Magnamon later kidnaps Dorugamon and extracts his data.
Dorugamon is left for dead in a junkyard and is taken into hiding by WarGreymon X's troops, including Wizardmon, Mummymon and Silphymon. The forces of Yggdrasil later attack and the Digimon defend themselves, Dorugamon eventually digivolving to his Ultimate Level, Dorugreymon. Gallantmon X and MetalGarurumon X, who somehow survived Omnimon's atrtack, later join the fight. Gallantmon X opens the way to Yggdrasil's domain where Omnimon and Magnamon await. Just as Omnimon was about to dismember Dorugreymon, DoruGreymon digivolves into Alphamon. Omnimon, intrigued by this revelation and persuaded by Alphamon, decides to confront Yggdrasil. Magnamon refused to go with them and states his loyalty to Yggdrasil but does nothing to stop them besides warning the super computer. Before they reached the chamber, Yggdrasil summoned DexDorugoramon, who was created by the data stolen from Dorugamon earlier) to fight them. Alphamon destroys the creature easily and he and Omnimon proceed to Yggdrasil's chamber. The to demand to know Yggdrasil's reason for destroying so many Digimon but the computer's only answer was to summon the remains of DexDorugoramon, which reconfigure to for Dexmon. The beast trapped Omnimon in its claws. When Alphamon tried to free Omnimon, he realized that Dexmon was his other half, born from Yggdrasil's extraction. Now knowing that they were one and the same, Alphamon impaled himself along with Dexmon with his sword, Ouryuuken. When Omnimon demanded why he did it, he explained how Dexmon was his shadow and that was what he would have become if he had not met his friends. With the last of his strength, he gives his X-Antibody to Omnimon, who consequently becomes Omnimon X, before reabsorbing Dexmon and regressing back into a barely alive Dorumon. Omnimon, his eyes now fully opened to Yggdrasil's injustice, raised his blade and destroys the computer with the All Delete attack. With the Digital World restored, Omnimon observed the landscape with his friend Gallantmon as the two pondered over why Yggdrasil did what he did. Gallantmon concluded that Yggdrasil, just like every other being, was simply trying to live. meanwhile, Dorumon returns home and is joyfully reunited with Tokomon X.展开