Leaving Alpha and Roland behind, the Gray Ravens comes upon a large cavern with a lethal concentration of Punishing Virus. They spot a gargantuan Hetero Creature, called the Polyphage, standing in the middle of a lake of Red Tide. The size and power of the monster are so great that if it makes its way to the surface, not even Babylonia would be safe.. Lucia leads the team to investigate the area and scout for a path of safe entry.
Before they can make much progress, they are contacted by Murray. He tells them of a transport pod located in one of the old factories and suggests they go there. Lee is suspicious of Murray's intimate knowledge of the underground city's layout. After the call ends, Lee asks Liv to analyze the background audio of the call. She finds that the call did not originate from Babylonia. Lee deduces that the "Murray" they just talked with is an imposter, trying to lead them into a trap. They suspect that it is most likely Lamia, the only Ascendant with the ability to turn invisible and shapeshift.
It's not long before "Murray" contacts them again and Lee accuses them of being a fake. "Murray" tries to find an excuse, but gives up all pretenses when the Commandant directly calls them "Lamia." Lamia claims she can safely guide the Gray Ravens to the Polyphage in exchange for Huaxu's key. Unable to trust Lamia’s words and with little time to spare, the Commandant orders the team to search for her.
The Gray Ravens quickly track her down and capture her without any resistance. They restrain her and have her guide them through the chasm. Another earthquake shakes the cavern originating from the Polyphage. It causes Lucia to believe something has happened to Luna.
They arrive at the epicenter, which is a crater of rubble. Lamia notes that Luna is the only Ascendant she knows who is capable of such destruction. The Gray Ravens are unable to deduce who Luna’s opponent was, so Lamia extracts a recording organ from a nearby Hetero Creature. The Commandant loads the information into the Spear of F.O.S.
A projection shows Gabriel and Luna standing before the Polyphage. Gabriel intends to have the Polyphage transform everything into the Red Tide, letting the Ascendants rule over the world devoid of all lifeforms. He admits that the Polyphage is missing a crucial component to becoming functional: an Ascendant.
Gabriel nominates Alpha, which causes Luna to react violently. Gabriel reminds her that all Ascendants are obligated to sacrifice for the Ascension Network. Luna refuses to abandon her sister, calling the Polyphage a fruitless attempt. The Ascension Network’s plan was to create a paradise for the worthy, not to rid the world of everything.
Gabriel says that the bodies of Ascendants are just temporary tools to accomplish greater things. His vision of the future is one where the Red Tide swallows everything and gives birth to Hetero Creatures that continually evolve to replace Ascendants and even Agents. He then introduces the Heterozygote Queen, a creature possessing power on par with an Agent that would act as a terminal for the Polyphage.
Luna challenges this new creature but has to expend a tremendous amount of effort to defeat it. Luna suspects that the power she receives from the Ascension Network is waning. Gabriel then attacks Luna from behind, accusing her of betraying the Ascension Network. He declares that she is no longer fit to be an Agent. Tentacles from the Polyphage wrap around Luna’s limbs and she is swallowed despite her struggles.
When the projection ends, the Gray Ravens hurry to the Polyphage. Lamia creates bridges out of the Punishing Virus to get over the wide gaps. She says that the Polyphage has become extremely powerful after devouring Luna. Liv theorizes that the only way to defeat the Polyphage would be to remove Luna from the Energy Core. In the middle of this, Lamia manages to melt her restraints. She attempts to steal Huaxu's key from the Commandant. Lee intercepts her, but she still escapes.
The bridges that had allowed them to come this far also crumble, leaving the Gray Ravens stranded next to the Polyphage. Sometime after her escape, Lamia is contacted by the true Murray and he speaks of the favor he owes her in exchange for helping the Gray Ravens.
The team arrives at the Polyphage and encounters Gabriel and the Heterozygote Queen. Gabriel blames Lucia for leading Luna astray from the path of a perfect Agent by allowing her to become sentimental. Gabriel had originally planned to have the Polyphage consume both Alpha and Luna, but Alpha never showed up. He informs the Gray Ravens that once the Polyphage fully fuses with Luna, it will show everyone that his vision for the future is the correct one.
Gabriel is disappointed that the Commandant cannot envision the same future as him. Before leaving, he summons vast amounts of Hetero Creatures from the Red Tide and sends the Heterozygote Queen to protect Luna. Lucia finds an opening to fire an ice blast that exposes and damages the Polyphage's core. Before they can celebrate, the Polyphage begins to repair itself. The team realizes that the only way to stop the Polyphage would be to remove Luna from its core.
Lucia confesses that despite the Ascendants being humanity’s enemies, she still wants to save her sister. Liv, Lee, and the Commandant are supportive of her wish. They refuse to let her go by herself.
Down below, Roland barely puts up a fight against Alpha. She finds this suspicious and asks about his intentions. Roland reveals Gabriel's plan: to feed Luna and Alpha to the Polyphage, as Gabriel believes them both to have betrayed the Ascension Network. Roland's desire to see Luna's wish fulfilled, so he delayed Alpha, hoping someone would remain to defeat the Polyphage. Before Roland can say more, Gabriel appears from the shadows. Roland retreats, leaving Alpha to face off against Gabriel alone.
Back above, Hetero Creatures hinder the Gray Ravens. Lee locates the Polyphage’s weak points and incapacitates its arms. However, the rate at which the Hetero Creatures spawn is too high—Liv and Lee stay behind to open up a path for Lucia and the Commandant to breach.
Meanwhile, Lucia and the Commandant arrive at the top of the Polyphage and see Luna trapped inside the Energy Core. The Heterozygote Queen attacks. Lucia and the Queen trade blows. The Queen gains the upper hand by copying and adapting to Lucia’s moves. When the Polyphage begins manifesting tendrils that attack alongside the Queen, Lucia throws the Commandant a case that contains a spare katana as she attempts to hold off the horde. The Commandant uses this blade to cut open the shell of the core.
The Polyphage and Queen are about to overwhelm them, but they suddenly stop moving as if they lost all direction. Unbeknownst to them, Roland had located another hidden Heterozygote Queen. He speculates that Gabriel had made a second terminal as a contingency plan. Roland defeats the copy before he falls unconscious.
Seizing the opportunity, the Commandant reaches inside, ignoring the lethal Punishing Virus concentration to link to Luna’s chaotic M.I.N.D. They arrive at a mental landscape that is an endless black void. A projection of Luna appears. She thinks the Commandant is a fake created by the Ascension Network to manipulate her. Her only wish is to create a world where Lucia doesn’t have to carry the burden alone.
The Commandant assures Luna that they are real and that they need her help to save Alpha and Lucia. The Ascension Network pushes the Commandant out of the M.I.N.D. connection. Luna, having regained consciousness first, wakes the Commandant. The Queen is overpowering Lucia, and Luna says that the only way for them to save her would be for the Commandant to connect their M.I.N.D. Beacon to Luna’s M.I.N.D. Despite the risks, the Commandant agrees.
The Ascension Network grants Luna more power when it perceives the Commandant’s link to her as a threat. The Commandant’s determination makes Luna ponder if a different path to a perfect world exists. She gathers up the Hetero Polymers and uses them to destroy the Polyphage’s Core. The blast knocks out the Commandant and Lucia.
When they regain consciousness, Luna is nowhere to be seen. The cavern begins to collapse. The Commandant tries to carry Lucia out of the cavern. However, a quake topples the platform they are standing on. Luckily, Bridget and the Support Force arrive to save them. They reunite with the other Gray Ravens and make a hasty escape.
This section of the story can only be unlocked by playing Chapter 13: Fake Ascension in Explore Mode.
The Gray Ravens acquire data that showcases the Red Tide’s rapid expansion. A Scavenger group is exploring the nearby ruins after hearing rumors that they contain supplies. Although there is a possibility that the information is unreliable, they have no other choice.
The group arrives and begins to search for supplies as well as a place to rest. As they finish settling down, they encounter an armed Scavenger group. One of the hoodlums intimidates the people. A young girl named Youle admonishes him, claiming that God will not forgive him. She lets slip the existence of an angel who informed her of the supplies. The armed hoodlum mocks Youle, then orders the rest to get to work.
One day later, the group discusses how they hear the sound of waves in their sleep. They also notice the disappearance of several Scavengers. As more and more people disappear, one of the Scavengers claims to have seen them in the Red Tide and wonders if they are now living in it.
A new Scavenger group arrives, bringing rumors of the Red Tide with them. The people come to believe that the Tide is humanity’s salvation—their final resting place. However, Youle refuses to accept that and continues to pray to God. A Scavenger mocks her, telling her that people will believe whatever they see, so long as redemption is an option. He then leaves in search of the Red Tide.
Over time, many fall prey to the Red Tide. Youle eventually departs the hotel. Although nothing seems to change, she continues to pray to God for salvation. In the end, Youle gives up. She allows the Red Tide to swallow her up.
