Three years after the events at Beacon Mental Hospital, Sebastian Castellanos has left the Krimson City Police Department to uncover the truth about the mysterious organization Mobius but 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. Drowning his sorrows in a bar, 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, though Mobius now needs Sebastian's help in saving her. Sebastian is then brought to a secret Mobius facility against his will 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, some time ago, Mobius lost contact with Lily and their agents inside Union, and they no longer have any control over the STEM. Sebastian reluctantly agrees to help Mobius so that he has a chance to save Lily and enters the STEM.