In the near future, humanity has been ravaged by a mysterious fungal disease (a mutation of Ophiocordyceps unilateralis). The afflicted are robbed of all free will and turned into fast, mindless flesh-eaters, referred to as 'hungries'. Humankind's only hope is a small group of hybrid, second generation children who crave living flesh but retain the ability to think and learn. The children go to "school" at an army base in the Home Counties, where they are subjected to experiments by Dr. Caroline Caldwell. Helen Justineau is responsible for educating and studying the children. The children are treated as prisoners, but humanized by Helen to the dismay of Sgt. Eddie Parks, although they are all restrained in cells, wheelchairs, and under constant armed guard. Justineau treats the children fairly and kindly, growing particularly close to a polite, exceptional girl named Melanie, who is shown to have a high level IQ. After Melanie reads a story she has written about a young girl saving a woman from a monster and the pair staying together forever (clearly drawing a parallel from her own feelings for Justineau), Justineau is overcome with emotion and affectionately strokes the girl's head. Parks bursts in and rebukes Justineau; he spits on his arm, rubbing off the masking gel, and holds it under the nose of one of the children, evoking a violent, animalistic response from the child that spreads to the others on that side of the room.As punishment, that evening Parks leaves Melanie restrained in her wheelchair in her cell, not allowing her to sleep in her bed. Helen visits Melanie in her cell, enters and starts to release her from her restraints, but the blocker has somehow worn off and Melanie reacts and starts snapping and trying to bite Helen. Melanie struggles to restrain herself, trying to retain her humanity to impress Helen, but is unable. Helen flees the cell, dropping her blocker lotion by the door, which is discovered later by Dr. Caldwell.Caldwell is revealed to be researching an antidote by experimenting on the children. Caldwell gives Melanie riddles and puzzles, which her high IQ allows her to solve with her exceptional logic and reasoning. One day Caldwell asks Melanie for a number between one and twenty - Melanie chooses thirteen, and the child in cell thirteen is then absent the following day. The next time Caldwell asks Melanie for a number, she is surprised when Melanie chooses her own cell number (four). Caldwell reluctantly takes her to her lab, whereupon Melanie sees a preserved brain belonging to child thirteen. As she is strapped to a table, Helen rushes into the lab and tries to intervene to save her as it is revealed that Caldwell intends to remove Melanie's brain and spinal column to develop a possible vaccine. Helen is tricked then easily disarmed but the base has been overrun as the fences gave way and the lab is breached before Caldwell can proceed. Caldwell's hand is cut by broken glass when a hungry tries to smash its way into the lab. Melanie escapes the lab but outside the hungries are everywhere and soldiers are being swarmed and violently attacked in a failing, chaotic mass breach.Melanie wanders stunned by what she sees, but then violently attacks and infects two soldiers who are trying to restrain Helen. Helen and Melanie jump aboard an escaping armoured van. Parks, Privates Kieran Gallagher and Dillon want to shoot Melanie, but Helen shields her and Caldwell insists she needs her. Melanie is muzzled and handcuffed to the gunner's chair atop the armoured vehicle and the group escapes into the wilderness. The group reach a river to collect water but are attacked by hungries who have come out of the woods. The group is surrounded. Helen removes Melanie from atop the vehicle and brings her inside. Parks is forced to shoot Dillon who has been bitten and has started to succumb to the quick-acting fungal pathogen. Parks asks Caldwell why the hungries tend to group, Melanie speaks up saying, "they must be lonely."As the van is now broken down, the group proceed to London on foot where there is greater likelihood of food and supplies and where they can better communicate with Beacon, a larger military base. They discover London (which is overgrown with wild, unkempt vegetation) populated with multitudes of dormant, unstimulated hungries. By using a gel that blocks their scent and moving quietly, they manage to sneak past the hungries, shooting several in the head along the way, eventually finding shelter in an abandoned hospital. Caldwell reveals to Melanie that "second generation" hungries were discovered after newborns killed their infected mothers by burrowing out of the womb. When they try to leave the next day, they realize the hospital has been surrounded by a greater horde of hungries, possibly from their gunfire the day before. Melanie offers to lead the hungries away - as she alone cannot be attacked, essentially by being one - and the group agrees. She wanders around the area, exploring houses and experiencing childish wonder at the domestic and everyday objects she has never before encountered. She chases and devours a cat, then captures a small dog to use as bait to distract and lure the hungries away from the hospital so the group can escape. After leaving the hospital, Melanie sees a poster of a cat, and stares at it while Helen asks her if she would like to have a cat. Melanie quips that she already had one.As they progress through London they come across a mass of decomposing, infected bodies encircling the completely overgrown BT Tower and sprouting seed pods. Caldwell explains to the group that the pods contain spores that if released could end humankind, as the fungal pathogen will become airborne and infect all who breathe. They find a solar powered military mobile lab whose crew has gone missing. It is revealed that Caldwell is suffering from blood poisoning from the arm wound she incurred when the hungries invaded the army camp, and will die soon. The group hole up, sending Kieran out to find food and Melanie asks to leave to find food for herself, as she is finding her urge to feed overpowering. Melanie discovers a group of feral, second generation child hungries, who've learnt to recognize uninfected humans from the scent masking cream, which they presumably learned by hunting the missing lab crew members. She returns to the lab to warn the group that Kieran, who is wearing the scent blocker, is in danger and is being hunted by the ferals.While Melanie is trying to explain Kieran's danger to them, radio contact is made with Beacon (the central army base), which reports that the fences have come down and they'll shortly be invaded. Helen and Parks set off with Melanie but arrive too late and find Kieran's body ravaged and the feral child hungries surrounding them. Melanie manages to scare and dominate the hungries by growling and eventually battling and killing their leader. Melanie tells Parks and Helen to pretend they are afraid of her and she pretends to claim them as "hers" and leads them to safety.When they return to the lab they are ambushed and knocked out by gas that a haz-mat suited Caldwell has released. A severely injured Caldwell, whose blood poisoning is giving her very little time to live, attempts to drag Melanie into the lab but Melanie awakens quickly, revealing that her second generation bio-system metabolizes oxygen differently allowing her to hold her breath much longer than the uninfected humans. Caldwell tells Melanie that she is dying of her septic wound and needs to find the cure before she succumbs, before the pods ever open, which will eventually happen when they are exposed to extreme heat or water. She tries to reason that she can save Helen and the human race for Melanie by making a vaccine. Melanie asks if Caldwell now believes Melanie is truly alive and feeling, rather than simply "mimicking human emotions" as Caldwell once believed. When Caldwell admits that she knows Melanie is truly alive, Melanie asks why her kind should die to save humanity. "Why should we die, so that you may live?" Melanie then threatens Caldwell with a bite and leaves the lab, running back to the centre of London where she sets the towering seed-pod structure alight, causing it to germinate en masse and release an immense cloud of airborne spores. Caldwell, meanwhile, has attempted to follow Melanie but is surrounded by the feral children and killed. As Melanie returns to the lab she finds Parks collapsed succumbing to the fungal infection of the released spores. Melanie is visibly upset, as she thought to keep him and Helen safe in the sealed environment of the mobile lab. Parks asks her to not let him succumb to the fungal virus and Melanie grants him his wish by regretfully shooting him. She returns to the lab to find Helen, standing just inside the hermetically sealed door, fearfully watching the spores fall around the lab.The film closes with a tearful Helen awakening, secure from infection in the airlock, but effectively a prisoner inside the mobile med lab. Outside, sitting on the ground are the second generation children of the school/prison at the army base, along with the feral children all waiting and collected together, kept sternly in place by Melanie. Helen begins speaking through a microphone on outside speakers, once again to educate and teach all the children. It closes with Melanie asking for her favourite, a story, and after being kindly declined by Helen says that they now have "lots of time" to hear one.