ElDoradimon and all the Digimon in the Holy Capital have appeared in the human world. The Digimon begin to panic but Baromon is able to hold them together. Gizmon renew their attack but MirageGaogamon and Rosemon defend the city. The Digimon are filled with hope when Yoshino tells them Masaru will arrive soon. Yatagaramon, Ikuto, Masaru, and Agumon make it to the human world and observe from a distance what has happened. Masaru tries to go help but Kouki has appeared. Masaru tells Ikuto to go help defend the capital and he does so. Kouki and Masaru rush each other. Masaru realizes there is something different about Kouki and sees him evolve to his mega level, BioDarkdramon. Agumon evolves to ShineGreymon and the two Digimon fight.

Rosemon and MirageGaogamon continue to fight the Gizmon attacking the Holy Capital. Pumpkinmon are inspired by the two and begin fighting the Gizmon as well. Meanwhile, Kurata and his soldiers watch on from a nearby bridge. Kurata orders more Gizmon to attack and Kouki to continue keeping ShineGreymon busy. He also orders for the second part of the operation to begin. Naval ships and a giant spear begin moving towards ElDoradimon.

BioDarkdramon tries to go after his true target, Masaru, but ShineGreymon knocks him out of the way and begins to fight with Masaru on him.

Miki and Megumi watch the battle from the coast. Chika and Sayuri watch the events unfold on television and we learn the government is giving all its resources to Kurata.

ShineGreymon and Masaru manage to catch BioDarkdramon by surprise but realize if they attack he can evade and the attack will strike a building. BioDarkdramon tries to destroy a building full of people but ShineGreymon jumps in his way and is sent flying to the ground.

Touma and Yoshino notice four battle ships have surrounded ElDoradimon and are firing beams at the massive Digimon. Baromon watches ElDoradimon cry out in pain and yells for them to stop. Baromon is shot by a Gizmon and his last words are for Masaru to take care of ElDoradimon. Touma realizes ElDoradimon has been pinned down by the beams and then they notice a giant spear/javelin is being flown in by helicopters.

On the bridge, hundreds of trucks open up to reveal another army of Gizmon. Thousands of them fly towards the spear/javelin and attack themselves to it. Touma orders MirageGaogamon to destroy the Gizmon and Rosemon to destroy the ships.

Masaru has just woken up after being knocked out by BioDarkdramon’s last attack. Masaru tells BioDarkdramon to come down there and fight him so BioDarkdramon knocks a building down on him. ShineGreymon pulls him out of the way.

Kurata watches his “Gizmon Javelin” being created from the bridge. The Gizmon Javelin is a weapon designed just for ElDoradimon.

ShineGreymon asks Masaru what they should do because his attacks will wipe out the city. Masaru says he’ll never give up and his digivice begins glowing. ShineGreymon is infused with a new power and punches the ground. He pulls out a weapon called the GeoGrey Sword. ShineGreymon is now able to fight back without destroying the city. He attacks BioDarkdramon with his new weapon and damages BioDarkdramon. BioDarkdramon uses Dark Roar but ShineGreymon deflects it into the bay. The two Digimon rush each other one last time and BioDarkdramon turns back into his human self. ShineGreymon and Masaru head off to take care of the Javelin.

The Gizmon Javelin is now ready to attack ElDoradimon. ShineGreymon and Masaru rush to ElDoradimon’s side. Kurata orders the javelin to be dropped on ElDoradimon. MirageGaogamon and Rosemon save numerous Digimon before they’re destroyed by the javelin. The Javelin crushes ElDoradimon and he is reduced to a digitama, then essence.

Kurata is pleased because ElDoradimon’s essence will be enough to complete his project.