Humanity’s first interstellar colony is being built on the planet Proxima II, and until supralight travel becomes cheaper the first wave of colonists are on their own, eight light years from Earth. An expedition is sent to the mountain range near the colony, but only one survivor returns, covered in the others’ blood and in a state of shock. The survivor, Jake Leary, then breaks out of the hospital and vanishes into the streets of the colony, and some time later bodies begin to appear, mutilated in unfathomable ways. Morale in the colony begins to suffer when police chief Fuller is unable to locate and arrest Leary, and rumours begin to proliferate; some believe that Leary has been possessed by an evil spirit, while others believe that the colony execs are responsible for the murders, using Leary as an excuse to get rid of potential unionists and “troublemakers”. Fuller follows a lead and nearly catches Leary with his latest victim -- but as he tries to enter the room there is an explosion of green light, and Leary and his captive have both vanished by the time Fuller gets inside...
The colony’s executive officer, Helen Percival, demands that the problem be dealt with, but doesn’t offer any suggestions as to how; instead she seems more concerned with asserting her authority over the increasingly restless workers. The workers’ unofficial spokesman, Clark, convinces Fuller to let him help, understanding that the situation will only grow worse until Leary is captured. Fuller sends Clark to the building site where the last two bodies were found to see what he can learn, but then thinks better of it and follows him. But when he arrives Clark is dead, mutilated in such a manner that it seems his very identity has been removed. Convinced that something evil is lurking in the cellar of the building site, watching him, Fuller rushes back to the executive base and transmits an ultimate-priority distress signal back to Earth before anyone can stop him.
The Doctor and Sam arrive in response to the signal, but Percival, knowing they can’t have arrived from Earth this quickly, concludes that they have an agenda other than investigating. The Doctor convinces her to let him help Fuller, but he doesn’t realize how dangerously paranoid she is; driven by an obsessive fear of failure and a total inability to relate to other people, she becomes convinced that the Doctor, Sam and Fuller are all conspiring to remove her from power. Sam learns that Percival had the bodies of Leary’s victims cremated before autopsies could be conducted and buried the report on his expedition. Convinced that Percival is covering something up, Sam breaks into her office and finds the Leary report; but Percival has planted a bomb in her office in case of intruders, and Fuller rescues Sam seconds before she burns to death in the resulting fire.
The Doctor, meanwhile, speaks with xenozoologist Joan Betts, who was once romantically involved with Leary and who is studying the semi-intelligent native Proximans. The Doctor learns that the Proximans’ numbers have been dwindling drastically in recent months, and concludes from their excellent mimicry skills that they are at least partially telepathic. The markings on their nest seem to indicate that they have focussed their telepathic powers upon the mountains -- as if they have been trying to pen something in. He attempts to link with the mind of the Proximan nest, and before they expel him for his own safety he learns that their group mind is under attack by something ancient and evil. Betts refuses to accept his wild theories, and when he confronts her about Leary she flees. Convinced that she knows where Leary is hiding, the Doctor follows her to the tunnels beneath the city -- but the thing which is waiting for her isn’t Leary, and it kills her and attacks the Doctor...
Percival orders her security officer, de Winter, to restore order and locate the missing Doctor, Sam and Fuller, and de Winter takes advantage of his remit to impose draconian restrictions on the ordinary civilians. As the workers fight back against the restrictions, the colony begins to tear itself apart -- and people go missing on the edges of riot zones. Sam and Fuller read the classified Leary report and learn that, if Leary’s journals are to be believed, his expedition has awoken something ancient and evil which had been hibernating in the mountains. Fuller and Sam are separated during a police action, and Sam spends the night on the colony streets. Fuller’s deputy Jeffries locates her and takes her back to Fuller, who has been hiding in a building site... or so it appears until Sam realizes there is something off about his behaviour. This “Fuller” is an impostor, a shape-shifter which has already killed the real Fuller. The creature kills Jeffries as well, but before it can kill Sam it is attacked by a native Proximan. Sam gets to Jeffries’ car and tries to drive to safety, but the shape-shifter attacks, and while trying to shake it off she drives into a security roadblock. The shape-shifter kills de Winter as it escapes.
The Doctor is found unconscious in the colony streets and brought to the executive offices, where he recovers and explains that the colony is under attack by an entity known to the Proximans as “F’Seeta”, Face-Eater. The shape-shifting servants of the Face-Eater have been killing colonists and draining their life essences for the Face-Eater to consume. It soon becomes clear that a shape-shifter has infiltrated the executive offices as well, and Percival retreats into a world of her own, too terrified of failure to do anything herself. Then Leary arrives and exposes the “Doctor” as one of the shape-shifters; Leary had been holding the real Doctor prisoner on the mistaken assumption that he was a shape-shifter. Leary’s expedition indeed woke the Face-Eater which dwells in the mountains, and he fled when it slaughtered his teammates. He then followed the shape-shifters back to the colony, and all this time, while the police thought he was the killer, he has been trying to track and destroy the shape-shifters.
The Doctor has gone to the mountains to confront the evil at its source, accompanied by a Proximan native. When the Face-Eater begins to assault him with mental attacks and illusions, the Proximan links with the Doctor’s mind to protect him, and the Doctor learns the nature of the threat through their mind-link. The F’Seeta is a biological defense mechanism, built by the native Proximans as a control unit through which to meld their minds into a gestalt in order to protect their world from external threats. But the central bio-organism grew greedy and began to consume all life on the world into itself. The few survivors managed to contain it at the cost of perpetual vigilance, until Leary’s expedition woke it again.
Percival decides that the danger is past now that the shape-shifters have been exposed and destroyed, and refuses to mount a follow-up expedition to the mountains, claiming it would be bad for public morale. Instead, she holds a public demonstration and attempts to blame Sam and Leary for the “disturbances”, using them as scapegoats to secure her position. Just as they’re about to be executed, however, the unfathomably huge Face-Eater explodes from beneath the surface of the planet, having finally fed upon enough colonists to attack openly. In the confusion, Percival rushes to the colony’s emergency systems and tries to trigger a nuclear airburst to wipe out all life. Sam and Leary try to stop her, but fail; fortunately, the satellite has already been disabled by one of her own employees, who was worried about her instability. Percival flees into the ruins of the colony and is killed by a disgruntled worker.
The Doctor confronts the Face-Eater, which attempts to absorb him into its gestalt; however, it is confused by the Doctor’s own gestalt nature, of numerous personalities dormant within a single collective entity. In its confusion, its hold over the Proximans it has drawn to itself over the past few months weakens; while they attack it, the Doctor locates its central control unit. Although the Doctor hopes to reprogramme the Face-Eater and enable the Proximans to co-exist with the human colonists, the Proximans insist that he destroy it and do so themselves when he refuses. With the Face-Eater destroyed, the colony is saved; but without their gestalt link the Proximans are nothing more than semi-intelligent mammals which will be unable to survive the human colonisation of their world.