Inside Space Paranoids, corruption caused by Kira's multiple infections has caused a Rampancy-like state.  She has forced open a portal to other cyber dimensions, causing many Black Guards from a parallel version of Space Paranoids to come through and attack.  Azumi Ian, Zero, Audrey Jones, Isaac Zivaku, Naito Zivaku, and a roped-in Damien Reid fight their way to the rampant AI, and Zero is consumed by the AI.  However, he manages to stun her from within, allowing Audrey to take the others (except Azumi and Tron, who stay behind to protect Kira's body) into K1-R4's subconscious. Zero is alone in the Rage stage of the Rampancy, which consists of the Maverick Virus, taking the shape of one of Wily's castle fortresses.  Audrey and Isaac appear in Melancholia, a deep dark cavern where they hear whispering voices and find a younger version of Kira.  Damien and Naito fall to Envy, a place made almost entirely of half-alive corpses, moaning and unable to die.

Zero fights his way through Wily's Castle, eventually coming to a boss room.  Inside is a version of Kira infect with Omega's anger, wearing his armor, and held on strings by Wily like a puppet. Zero manages to defeat her, but takes heavy damage during the process.  Audrey and Isaac follow the cowardly version of Kira, who has mistaken them for Cortana and Sain, and their scenery changes, with a different Kira speaking to the monstrous Gravemind.  After a while, they then appear in a forest once consumed by the Gravemind, where a mass of Flood chase them then through a city full of people.  Then they are in a shack, and then a library, and then back to the Gravemind, who closes off the tunnel and consumes this Kira.  Marathon Eva appears, but Audrey uses her Dream Magic to take them away.  Damien and Naito attempt to make their way through the mountain of bodies, having to work together to conquer obstacles, including a maze which Naito goes through while Damien operates levers and machinery on the outside, though Naito is still harmed by countless traps.  However, the Firewall blocks them off from their final goal, and though the two manage to get past it, it grabs Naito.  Damien, too weak and unable to do anything to help, Has to leave him behind.

They all appear in a white void, with floating text in code.  Naito managed to escape, and Isaac hurts Damien for leaving him behind, even though he couldn't do anything.  Zero is able to translate the code, when it turns out to be a  passage from the Illiad.  Damien, despite his near-mad state, deduces the deeper meaning behind the passage, and discovers that Kira wants to be deleted.  They all agree to find another option, and choose the correct doorway out of Kira's mind.

On the outside, the viruses that were expelled from Kira form to become the Firewall, and the group attack it, with a headless Kira reforming slowly.  Zero is damaged during the fight, and his form is corrupted by the Firewall, making it appear more like a virus.  Eventually, though, the Firewall is defeated, but only to be replaced with a second form, the same that Naito and Damien faced while in Kira's mind, called Marathon Eva.  Though seemingly defeated, Zero and Kira manage to merge together into a new form, called KZ, that manages to fight back and defeat the monster.  Without the viruses attacking Space Paranoids, the portal becomes stable, and Kira merges the remnants of the Firewall and Marathon with the system itself, making them unable to ever reform a consciousness.