Three weeks after the “Horde” incident,[a] David Dunn, a superhuman who survived the Eastrail 177 train wreck nineteen years ago,[b] now operates as a vigilante dubbed the “Overseer” alongside his son Joseph. Together, they track down Kevin Wendell Crumb, the “Horde”, at an abandoned factory where he holds four cheerleaders hostage. David engages Kevin in a brief battle until armed forces led by Dr. Ellie Staple intervene and imprison them at the Raven Hill Memorial Mental Institute. Also being kept there is David’s “destined” foe and global terrorist Elijah Price, who is kept under sedation and is considered completely harmless.

David and Kevin are placed into separate rooms that contain unique security measures based on their specific weaknesses. Staple explains that she believes they suffer from delusions of grandeur and do not have superpowers. Elijah’s mother Mrs. Price, Joseph Dunn, and Casey Cooke, a victim who survived Kevin/the Horde’s captivity, try and fail to convince Staple superhumans are real. As part of her final evaluation, Staple brings the three men to a room where she challenges them with explanations of why their seemingly superhuman abilities are not extraordinary. Kevin and David become distraught while Elijah remains catatonic. That night, Elijah escapes his cell to conduct research on Kevin before visiting him and telling him he feigned his sedated state and plans to escape the institute but requires one of Kevin’s personalities—the Beast—to help him. Staple discovers Elijah’s escape plan and proceeds to do a prefrontal lobotomy to silence him.

Upon returning to his cell, Elijah reveals he sabotaged the surgical laser and kills his caretaker Daryl before freeing Kevin. Elijah then manipulates David into fighting the Beast by revealing his plan to destroy a chemical lab inside a new skyscraper in Philadelphia that would kill thousands. David breaks free from his cell and pursues The Beast. Mrs. Price, Joseph, and Casey arrive just as the trio escapes. David and the Beast fight for a while before Elijah reveals to The Beast David’s weakness for water, after that Joseph reveals that Kevin’s father died in the train wreck caused by Elijah Price nineteen years earlier. Despite thanking him for his creation, the Beast mortally wounds Elijah out of distrust, and throws David into a water storage tank that drenches the area when he gets out. Casey manages to bring Kevin’s dormant original personality out, inadvertently allowing the police to fatally shoot him. Staple’s men drown David in a flooded pothole while Staple reveals that she is part of a clandestine organization that has been suppressing the existence of superhumans for millennia to keep people from knowing about them and killing those with superhuman abilities as they see them as a threat to the balance of the world.

In the aftermath, Staple deletes the footage from the institution, only to realize Elijah had secretly live-streamed the events to a private network. Mrs. Price, Joseph, and Casey all receive a copy of the footage and upload it to the public, exposing the existence of superhumans to the world.