Kevin (James McAvoy) kills Elijah (Samuel L. Jackson) after discovering that Elijah derailed Eastrail Train 177, which his father was on.
Dr. Ellie Staple (Sarah Paulson) orders a SWAT team to kill Kevin and David (Bruce Willis) because she is part of a secret society called the Clover that has been quietly killing superhuman people over the decades. She erases all evidence of their stay at the hospital, however, before his death, Elijah sends security camera footage of Kevin and David’s battle to Joseph (Spencer Treat Clark), Casey (Anya Taylor-Joy) and Elijah’s mother (Charlayne Woodard), who publish the footage online so that the world of superheroes will be known to the world.
A psychiatrist named Dr. Ellie Staple brings together the invincible David Dunn, his nemesis Elijah Price/Mr. Glass, and Kevin Wendell Crumb/The Horde to her facility, Raven Hill Psychiatric Hospital, to convince them that they are not actually superpowered and are merely suffering from delusions brought on by past traumas. Elijah wants to join forces with Kevin and bring forth his Beast persona to inflict harm upon the world.
Elijah manages to get The Beast on his side as they plan to head to the opening of a new skyscraper to kill many people. David breaks out of his room to stop them, leading to a fight witnessed by Elijah’s mother, David’s son Joseph, and The Horde’s surviving victim Casey Cooke. Joseph turns The Beast against Elijah when he reveals that Kevin’s father was on the same train that Elijah derailed wherein David was the only survivor. The Beast mortally wounds Elijah by shattering his bones before he fights David. Casey manages to get Kevin to go back to normal, but this leaves him vulnerable and one of Staple’s men shoots him in the abdomen, and he dies in Casey’s arms. David is then drowned in a puddle, but not before he touches Staple’s hand and learns she is part of a secret organization that wants to prevent superpowered people from walking among society.
Although Staple thinks her operation was a success, she later learns that Elijah deliberately escaped via the tunnels in order for the surveillance cameras to record himself, plus David and Kevin. The footage is uploaded to the web by Casey, Joseph, and Mrs. Price, and they watch as the world learns about the existence of the superpowered.
The film starts with Kevin Wendell Crumb (James McAvoy) in his Patricia persona talking to four high school cheerleaders that he kidnapped, attempting to ease them with one of his more comforting identities.
Elsewhere in Philadelphia, two punk teens jump an unsuspecting man for the sake of making a dumb internet video. David Dunn (Bruce Willis) follows them to their home and stalks them in the darkness before he beats them up for hurting another person. David later goes to join his now grown son Joseph (Spencer Treat Clark), who has been helping him over the years to catch crooks through surveillance footage. David’s acts have gotten the media to label him “The Overseer”. They are currently tracking The Horde in the hopes of finding the kidnapped girls and stopping more murders from happening. Outside of their work, David has been missing his wife Audrey, who has since left him.
Later on, David takes a walk around town, brushing up against people in the hopes of tracking down The Horde via skin contact. He comes across Kevin as Hedwig and brushes past him, catching a glimpse of him in the location where the girls are being kept. He contacts Joseph and follows Kevin. David arrives at the location and frees the girls, just before Kevin returns as The Beast. The girls start to run away, but The Beast hurls a table at one of the girls, injuring her. David fights The Beast until the two fall out a window. A bright flash of light hits Kevin, snapping him out of the Beast persona. They are faced by a group of armed men, led by Dr. Ellie Staple (Sarah Paulson). They apprehend Kevin, but since Staple claims that David has hurt people, they take him with them as well.
David and Kevin are brought to Raven Hill Psychiatric Hospital where Staple wants to research them. She claims to specialize in a particular kind of psychiatry for people who believe they have superpowers. David is placed in a room that will trigger multiple water hoses to spray him if he is perceived as threatening, while Kevin is in a room where flashing lights will cause him to revert to a less harmful persona if he attempts to snap into The Beast. Also living in the facility is Elijah Price, AKA Mr. Glass (Samuel L. Jackson), whom David still remembers as being responsible for causing the train crash that only he survived, though Elijah has been kept heavily sedated this whole time.
Casey Cooke (Anya Taylor-Joy) has returned to school following her capture, now known by her fellow students as the girl who got away from Kevin. She is called into the principal’s office to be informed that Kevin has been captured.
Kevin is visited in his room by Daryl (Adam David Thompson), an employee of the facility. Kevin takes on a flamboyant persona to tease Daryl before switching to Scottish twins. Daryl starts to flash the lights manually to keep Kevin away until he turns into Patricia and is elegant and composed.
David gets sprayed with water until he is weakened as he had tried to make an escape. He tells Staple that he needs to get out to stop Kevin, but she assures him that Kevin is secured.
Staple has separate meetings with Elijah’s mother, Mrs. Price (Charlayne Woodward) over her son’s condition and personality, as well as Joseph over his work with his father. She continues to assert that David is as harmful to others as the people he tries to stop, and that she wants to snap him out of his delusion or he will remain institutionalized.
Casey later visits Raven Hill to see Kevin as Hedwig, who still views Casey as his girlfriend. Staple thinks that Casey being there and showing Kevin affection will allow him to be Kevin and not an alternate persona. Casey succeeds in bringing Kevin out, and she tells him that she put her abusive uncle in jail for what he did to her. Kevin starts to break down and eventually reverts to a different persona.
Staple decides that for her final evaluation, she will bring all three of her subjects together in the same room. David becomes distressed when he comes face-to-face with Elijah after all these years. Staple tries to convince the men that their so-called delusions are a result of traumas in their life. For David, it was an incident in his childhood where some kids tried to drown him in a pool. For Kevin, it was years of abuse at the hands of his mother after his father died. Staple also apologizes to Elijah for how he was being mishandled.
Casey and Joseph make separate trips to comic book shops to get a better idea of the cases involving Kevin and David. Joseph also does some digging into Kevin’s past to learn about his father.
Another facility employee, Pierce (Luke Kirby) goes into Elijah’s room with a flashlight and jokingly lets it slip to drop onto Elijah’s legs before Pierce catches it. He says he is there to check on Elijah since he left his room the night before. Not long after, he sneaks into the surveillance room to read Kevin’s file. He then goes into Kevin’s room and speaks to Patricia. Elijah says that Staple’s work won’t prove that their extraordinary abilities don’t exist, and he is also hoping to meet The Beast.
Elijah goes back to his room to sleep, but is later woken up by Staple, who tells him she saw him leaving his room via surveillance footage and is taking him to get a procedure done on his frontal lobe. This triggers a memory from Elijah’s childhood where he was at an amusement park on a ride by himself, and one bad movement broke his arm.
After Staple leaves, Elijah is visited in his room by Daryl. Elijah takes a concealed shard of glass and uses it to slit Daryl’s throat. He then leaves his room again and goes to meet The Beast. He deems Elijah as pure for his condition, and he agrees to follow Elijah in his plan to have a bad guy team-up. Elijah uses the intercom to tell David that he has turned the water off, and he threatens to kill many people if David doesn’t manage to break himself out of his room.
Pierce sees Daryl’s corpse on the security cameras. He finds Elijah in a storage room where he and The Beast trap him. The Beast sees Pierce as evil for hurting Elijah, and he squeezes Pierce’s body until he severs his spinal column and kills him. The Beast wheels Elijah out of the facility through the tunnels where they are found by three guards. Elijah rolls himself away while The Beast disposes of the men violently. Meanwhile, David succeeds in breaking the door down and leaving his room.
Staple finds Daryl dead and deduces that Elijah and The Beast are headed to the newly unveiled Osaka Tower, knowing that a large crowd of people will be gathered there. She dispatches her men to stop them before they leave the premises. Casey, Joseph, and Mrs. Price all appear at the facility as well to witness the confrontation. David emerges and battles The Beast, dealing mighty blows against one another. Joseph steps in to talk to The Beast to inform him how his father died: he was on the very same train that Elijah derailed that David survived. The Beast directs his ire toward Elijah for his deception, while Elijah tries to defend his position by saying it had to happen for The Beast to be born. He crushes Elijah’s shoulder and causes him to fall out of his wheelchair, shattering more bones in his body. The Beast then continues to fight David and throws him into the water storage tank right before it bursts and frees them.
Casey reaches The Beast and calls him by Kevin’s full name. It brings Kevin back to normal, but now that he is vulnerable, one of Staple’s men shoots him in the abdomen. Kevin’s multiple personalities (primarily Hedwig, Patricia, and Barry) come out one last time as he dies in Casey’s arms. David, still weakened by the water, is taken by two of the mercenaries and has his head shoved into a water-filled pothole. Staple approaches him, and David touches her hand. He sees that she is part of a secret organization, all with matching clover wrist tattoos. She explains to him that the organization is devoted to keeping superpowered people hidden from the public eye, and that the superheroes need to die to prevent the rise of the supervillains. She asks David if she ever convinced him that he was a normal man. The men then finish drowning David in the puddle. Joseph runs to his father’s body and weeps. Mrs. Price goes by Elijah, who assures him that he was not a mistake, right before he too dies.
Staple later addresses her cohorts to declare their mission a success. She then goes to a comic book shop where she overhears two patrons talking about one particular villain known as “The Mastermind”, as he manages to get people to look the other way while he sets his true plan in motion. This makes Staple realize that Elijah had a bigger plan all along. She goes back to the facility and realizes that Elijah deliberately escaped through the tunnels in order for the cameras to record him, as well as David and Kevin. The footage was uploaded to the internet, meaning the world will now be aware of the existence of superpowered people. Staple leaves the surveillance room and screams in defeat.
Casey, Joseph, and Mrs. Price gather at a station as they have uploaded the footage to the web. They sit and wait as people around them watch the video before it hits the news, meaning that the legacies of their loved ones will not have died with them.