Dorumon is running from Leomon. It seems that Leomon wants to kill him. When Leomon catches up he doesn't kill him. He digs his sword down in front of Dorumon into the ground stating that he isn't Dorumon's enemy and that Dorumon should live for him. Leomon then does what most Leomon do in Digimon - dies. Dorumon screams as the storm continues around him.

Dukemon + Omegamon (2 of the Royal Knights) are talking about a thing called Project Ark. Dukemon is wondering if they are doing the right thing with Yggdrasil killing many Digimon.

Andromon, Blossomon, Hanumon, and Tokomon (who is just there) are having an argument with War Greymon, Garudamon X, and Kokuwamon X. It is about if all Digimon are going to die. Garudamon X explains that with the dying they had to take the X Antibody to survive the purge and Yggdrasil is the enemy not them. Andromon reveals that he has transmitted the conversation to Yggdrasil

Omegamon appears in a ticked off mood. He proceeds to start blowing a ton of stuff including Digimon. Garudamon X flies up but is shot down. WarGreymon X attacks but is soon shot down by Omegamon. Omegamon also decides to kill Blossomon, Hanumon, Andromon, Tokomon, and WarGreymon X. The first ones are destroyed rather quickly leaving WarGreymon and Tokomon. WarGreymon X then starts fighting Omegamon once more and doesn't do all that well. He decides to run from Omegamon carrying Tokomon all the way.

WarGreymon X takes a huge blast, and is sent flying through the moutains. He crashes into a building that Dorumon happens to be staying in. Dorumon comes out, sees WarGreymon X, talks to him. WarGreymon X flies off leaving Tokomon behind with Dorumon.

WarGreymon X and Omegamon end up duking it out again. While WarGreymon X is in water Dukemon contacts Omegamon, They talk for a bit before Omegamon flies off leaving WarGreymon X in the water. Magnamon, Omegamon, & Dukemon talk again about Project Ark and that Yggdrasil is not to be questioned (like Dukemon is). There's obvious tension between the Knights.

WarGreymon X has survived and makes it to nearby cave where Metal Garurumon X is based. War Greymon X tells Metal Garurumon X that they Royal Knights are strong. Metal Garurumon X wonders if the Royal Knights are the true enemy and refuses to fight until he knows for sure.

Then we go to a scene where Dorumon and Tokomon are standing in a forest. Over the mountain in the distance is a stampede! It's a bunch of Digimon, running from Omegamon. They are all deleted except a very injured Triceramon, and Omegamon walks up and then squishes it's head with his foot. The horn pops off thus he is deleted.

Dorumon and Tokomon watch everything. Dorumon makes a noise that catches Omegamon's attention. He shoots in the area where they are and finds them. Dorumon tries attacking for all the lack of worth it does. Tokomon then tries and naturally it doesn't work. This keeps happening until both Tokomon and Dorumon are lying on the ground. Omegamon raises his sword to rid of them for good when Metal Garurumon X appears

Metal Garurumon X asks Omegamon if this is the Royal Knights Justice. He is told no it is Yggdrasil's Justice. Metal Garurumon X now decides that the Royals are the enemy attacks. War Greymon X arrives and attacks as well. Omegamon's attack heads of Dorumon & Tokomon. Dorumon claims Tokomon is already dead. Metal Garurumon X saves Dorumon by shielding him from the blast. He then gives his X-Antibody to Tokomon (now Tokomon X) so that he survives.

Dorumon remembers that Leomon died for him to live. He evolvs to Dorugamon who attacks Omegamon. Omegamon asks him why he is attacking. He is told that it is because he wants to live. War Greymon X attacks as well. Omegamon goes to attack them both when Dukemon arrives. He has no wish to fight Omegamon but says about X-Program and that it was activated because there were too many Digimon. Omegamon is having none of it speech and practically calls him a traitor to Yggdrasil. They go into the clouds and fight. Omegamon impales Dukemon through the chest and deletes him. (justice for his betrayal)

Magnamon & Omegamon are together and talking again. Magnamon goes and captures Dorugamon & Tokomon X. Magnamon goes to kill Tokomon but Dorugamon uses his power to break free to save his friend Tokomon X. Dorugamon is then recaptured and taken the Royal Knights meeting place. There his data is split and is sent off. Tokomon X finds War Greymon X and explains what has happened and breaks down into tears. Wizarmon and Mummymon find Dorugamon and try to help him out of a pile of junk. We then see the other half of Dorugamon's data and with the evil music playing we know something bad is about to happen.

Wizardmon, Mummymon and Silphymon find out from War Greymon X who Dorugamon is and they to say the least are dubious about helping Dorugamon (cause of the RK's) but they do so anyhow. We then see Death-X-mon with a lot of Digitamas and one hatches into Death-X-Dorugremon. War Gremon X + Tokomon X head for Dorugamon when they see MANY Death-X-Doruremon who start to attack the area with Dorugamon in it. Out of no-where Metal Garurumon X appears (the hell he died!) and fights. War Greymon X & Tokomon X also arrive. War Greymon X attacks as Dorugamon is running through the cave. Mummymon gets ready to attack. Metal Greymon X makes it through after Dorugamon.

Tokomon ends up meeting Dorugramon who sees all the injured. He evolves to Dorugremon and joins the fight. He looks at his how reflection in the lake and is suprised to see who he is. He also gets pretty trashed in fighting. It appears that the 'rebel' digimon are winning against the Death-X-Dorugremon until a new swarm of them arrive. Omegamon says the Royal Knights part of Project Arc is about to start. Magnamon tells him to wait but is ignored. Dukemon reappears sporting his X-Antibody - ala Dukemon X.

Most of the Digimon head off for safety. Dukemon X opens a porthole for Dorugremon to go to meet Yggdrasil to find out the truth. Magnamon & Omegamon talk again in their meeting place. Magnamon basically asks Omegamon if he is going to leave Yggdrasil and is replied by a no that he is loyal. Dorugremon then arrives from the porthole and once again a fight with Omegamon ensures. Dorugremon is beaten and has his wings sliced off. As Dorugremon is laid on the ground he still won't quit. Omegamon goes to give the fatal blow as he refuses to let Dorugremon go to Yggdrasil. Dorugremon's thoughts of Leomon & friends go in his head again.

Cut back to the fight. Death-X-Dorugremon are flying about and now whatever they touch each other they seem to vanish. From Dukemon X's porhole a lot of rainbow colours are shown!

Dorugremon is evolving again to his final form. Omegamon and Magnamon are in shock and recognise the newly evolved Dorugremon to be a Royal Knight. His name is Alphamon. Omegamon and Alphamon go off to Yggdrasil leaving Magnamon alone. The Death-X-Dorugremon are destroying the Digital World. It is clear that Dukemon X and the others are badly beaten.

Omegamon and Alphamon meet Death-X-Mon. Omegamon goes to attack but is swiftly beaten. Alphamon attacks and takes down Death-X-Mon. The two digimon go into Yggdrasil's chamber to speak to him. Yggdrasil does not speak with them. They prepare to attack Yggdrasil, Death-X-Dorugremon along with Death-X-Mon come crashing in and grabs Omegamon.

Each attack Alphamon gives comes back at it's sender. Alphamon uses his Ultimate War Blade King Dragon Sword and forces the release of Omegamon. Throwing his sword back and then charging towards Death-X-Mon the sword impales himself as well as Death-X-Mon. They land on Yggdrasil as Alphamon asks Omegamon if he wants to become an X Digimon. Omegamon takes the X-Antibody as Alphamon & Death-X-Mon disappear. Omegamon X then gets peeved with Yggdrasil and destroys him. The Digital World then goes back to normal. Dukemon X & Omegamon X talk about how Yggdrasil controlled them.

Tokomon X is looking sad until someone is running towards him, the little guys face becomes happy as he sees - it's Dorumon! The movie ends with the duo being together.