However, the plan went awry when Theodore decided to kidnap Lily for himself. She reveals to him that she, Kidman, Theodore, and Myra had conspired to break Lily out of STEM and destroy Mobius from within. Sebastian, mistrustful of Theodore, refuses and is banished to a forest outside Union where he meets with Esmeralda Torres.

Sebastian is then approached by Father Theodore Wallace, who attempts to convince Sebastian to join him to seize Lily from Myra since Stephano betrayed him. Sebastian kills Stephano, but is shocked to see Myra spirit Lily away. Sebastian tracks down Stephano, who reveals that he had originally kidnapped Lily under orders from another party, but decided to keep her for himself to exploit her powers as the Core.

Another surviving Mobius operative, Yukiko Hoffman, explains that Stephano's status as a pyschopath gives him a measure of control over the STEM, granting him his powers. As Sebastian follows her trail, he realizes that Lily has been kidnapped by the photographer, who reveals himself as Stephano Valentini, a serial killer who had managed to infiltrate Union. He manages to meet Liam O'Neal, a surviving Mobius agent who helps Sebastian track Lily's whereabouts. In addition, Sebastian witnesses a mysterious photographer with supernatural powers hunting down and murdering Mobius operatives. Upon entering Union, Sebastian quickly finds that the town has been turned into a nightmare realm where all of the inhabitants have either been killed or mutated into bloodthirsty monsters. Sebastian reluctantly agrees to help Mobius so that he has a chance to save Lily and enter the STEM. However, some time ago, Mobius lost contact with Lily and their agents inside Union, and they no longer have any control over the STEM.

Sebastian is brought to a secret Mobius facility where he meets the Administrator, who further explains that Lily is being used as the Core for a new STEM system to simulate an idyllic town called Union. However, Mobius now needs Sebastian's help in saving her.

Sebastian is then approached by former partner and Mobius agent Juli Kidman, who reveals to him that Lily is still alive since Mobius faked her death. Three years after the events at Beacon Mental Hospital, Sebastian Castellanos has left the Krimson City Police Department and continues to be haunted by his experiences at Beacon, the disappearance of his wife Myra, and the death of his daughter Lily in a house fire.

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