Having defeated MegaMan, Bass attempts to steal his Ultimate Program but ProtoMan arrived just in time to prevent that from happening. Knowing how strong Bass is, ProtoMan set up a distraction, allowing him to grab MegaMan and escape. However, Bass easily catch up to them. Since ProtoMan also had a Ultimate Program, Bass targets him as well. MegaMan wakes up to see Bass grabbing ProtoMan by the neck and fires his Buster at him but Bass easily deflects the shots back at him. Lan and Chaud arrives just in time to help their Navis. MegaMan transform into Proto Soul and the two of them are be able to force Bass to retreat.
Lan and Chaud head to SciLab to inform them about Wily's message and about the can he gave them. Upon further inspection, Mr. Famous is able to safely announce that the can isn't a bomb. When the can was open, all they found was Wily bragging about WWW's former glory. In the meeting room, everyone discuss their plan on how to defeat Duo. Lan suggest that they used the same way Mr. Famous sent MegaMan to the Lunar Base during the PlanetMan incident to send MegaMan and ProtoMan to Duo's comet. Everyone agrees to the plan and heads to the Space Center. Before the duo can jack in their Navis, Bass arrived in Kid Grave's body and jacks in himself. As he is approaching to the comet, something was sent from the comet and is heading towards Bass. Inside the hyper route, Bass was suddenly attacked by a mysterious being.
Once Bass is dealt with, the being introduced herself to be Slur, Duo's subordinate. Slur confirms to the humans that Duo is indeed here to erase Earth when she is attacked by Bass. With most of the machine in the control room damaged, there is no way to send MegaMan and ProtoMan to the comet. Just then, reports of giant viruses appearing around the world was received. With time running short, Commisionner Kifune request that a Dimensional Area is put around the Space Center to prevent the viruses from attacking. Meanwhile, the viruses begin wrecking havoc around the world with a few people witnessing the attacks including Raika, a helicopter pilot, a boy with aboriginal origins, a young girl from Choina, a war veteran on wheelchair, Princess Pride, a rich woman and Maylu and the rest of Lan's friends. The battle between Bass and Slur continues but in the end, Slur is able to defeat her opponent and sends him deep into the Undernet.
Once the Dimensional Area has been activated, Lan and Chaud perform Cross Fusion and defeat the viruses attacking the Space Center. Suddenly, the two of them find themselves teleported into space where they watch a planet similar to Earth being destroyed. The planet is revealed to be Duo's homeplanet which he destroyed after its technology was being misused. Duo reveals himself to the heroes and was surprised to see two human/Navi hybrids. The heroes tells him about Cross Fusion and their duty to protect the Earth and threatens Duo to leave. Duo however wanted to test the humans further and see how powerful Cross Fusion really is. To this, he gave Lan a crest on his hand before sending them back to Earth. At the same time, he removed the viruses around the world and reversed the damaged that had been done.
Lan and Chaud find themselves back on Earth with Lan being able to see Duo's Comet while Chaud couldn't. Meanwhile, Dr. Hikari realize that the can Wily gave him contains microscopic blue prints on it that give them the plans to build a Dimensional Generator which will surely help them in future Cross Fusion battles. While the adults wonder what is Wily's true intentions for helping them, the scene shifts to Wily who wanted to prevent the Earth from being destroyed so he could enjoy his life longer.
- Yuichiro Hikari
- Lord Wily
- Mr. Famous
- Some of the future members of the Cross Fusion team made cameo appearance in this episode.
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