The TARDIS materialises in the grounds of a Victorian country manor on a peaceful midsummer day, but past experience has taught Ace that the idyll will soon be broken. Indeed, moments after the travellers arrive, the groundskeeper Ted is eaten by a tree and the gardener Alleyn is strangled by his own prize-winning roses. Young Victoria is attacked by an unearthly insect which lodges itself in her throat and begins to drain the life out of her. The Doctor and his companions find the dying girl, and as Ace leaves to find help, the Doctor tries to remove the insect but is distracted by its hypnotic, high-pitched whine. Victoria’s sister Charlotte and the housekeeper Mrs Irving arrive, but are unable to comprehend the horror they’re witnessing. Benny and the Doctor help them to carry Victoria back to the House, and as they do so, Benny catches a glimpse of a man standing by the lake -- a man who appears to have smoke pouring out of his body.

The Doctor is unable to remove the insect without tearing the flesh of Victoria’s throat. Victoria dies, but as the Doctor tries to break the news to the House’s occupants, he finds that they are unable to understand what is meant by “death”. The House’s occupants don’t even know where they are in England; they have no understanding of death or change, and know only of the House and its eternal summer. Benny and Charlotte take Victoria’s body to her room, but as Benny begins to question Charlotte, seeking an explanation for the House’s strangeness, the hedges on the balcony come to life and attack them both. Benny and Charlotte fight off their attackers, but as they retreat Benny realises that Charlotte has aged ten years in as many minutes; soon, she has changed from a teenage girl to a mature, middle-aged woman. Meanwhile, the Doctor hears a voice in his head telling him to leave, but is determined to remain and solve the mystery. He falls asleep in the living room, and dreams about an ancient Gallifreyan parable of a traveller whose curiosity leads him to destruction. As he wakes, night falls over the House for the first time ever, and Victoria comes back to life and eats Mrs Irving.

As Ace searches for help in the fields around the manor, her combat suit suddenly rusts to pieces. She meets a farmhand named Arthur, but as she tries to explain the situation to the uncomprehending young man, they are attacked by a monstrous combine harvester. While fleeing, they are sucked down through the earth and expelled into a muddy, rainswept field. Arthur faints, and Ace takes him to the nearby pub, where she is forced to fight off local thugs Archie and Thos Lewis. The brothers retreat, intending to report the newcomers’ arrival to their boss, Dr Stephen Rix; meanwhile, Ace convinces young ghost hunter Richard Aickland to take the ailing Arthur to his room to recover. Aickland is intrigued by Ace and Arthur, and wonders if they are connected to the ghost of Wychborn House, a manor gutted by fire in 1868. Arthur’s body starts to glow, but before Ace or Aickland can react the Lewis brothers arrive with their associates Billy, Frankie and Grey. In the struggle which follows, Archie breaks Ace’s neck, but the delirious, glowing Arthur lays his hands on her and brings her back to life. Arthur then loses consciousness again, and the confused thugs take them all to Rix for questioning while the pub’s terrified landlord, Bert Robbins, stands by helplessly.

The House’s butler, Garvey, tries to lay out dinner as if everything were normal, but the food rots away within seconds. Charlotte, Benny and the manservant Peter are then attacked by the spiderlike thing which was once Victoria, and while fetching wine from the cellars, Garvey is attacked by the thing which was once Ted. He fights it off, and finally realises that things have changed and that he must change as well in order to cope. He thus transfers his allegiance from the House itself to its inhabitants. As dawn breaks unnaturally fast and leaves fall from the trees en masse, the Doctor asks Benny and Charlotte -- whom he finds oddly familiar -- to investigate Benny’s vision of a burning man. At the lake, Benny and Charlotte find a travelling medical caravan owned by a man who calls himself the Quack. The Quack claims to be the dream of a doctor, and reveals that his medicines are poisoning the lake. He then transforms into an infernal steam engine, and as screeching monsters burst out of the forest, Benny and Charlotte flee back to the House. Just as they seem to have reached safety, hoewver, an insect like the one which killed Victoria flies into Benny’s mouth and stings her into unconsciousness.

Ace, Aickland and Arthur are brought before Rix, a former doctor who lost his sanity when his wife died giving birth to a deformed son. Rix believes that God is responsible for the pain in the world, and he was forced to leave Edinburgh under a cloud when he began experimenting upon vagrants to find the source of human pain. He has continued his work in this village, using his hired thugs to collect “specimens”. When he learns that Arthur brought Ace back to life he demands that Arthur heal his son, forcing him to obey by threatening to kill Ace and Aickland. But Arthur is weak and confused, and his touch inadvertently transforms Rix’s child into a spider-like monster. In the ensuing chaos, Arthur is shot and falls out of the window, and he flees, disoriented, towards the ruins of Wychborn House. Thos accidentally shoots and kills Billy while aiming for Ace, but Rix decides to keep her alive as a hostage, and breaks her fingers to prevent her from escaping. He orders Thos to dispose of Aickland, but Bert the landlord overcomes his fears and shows up just in time to save him. Thos shoots Bert, but Aickland escapes and follows the fleeing Arthur to Wychborn House.

The House is now occupied by the forces of evil. The thing that was Mrs Irving breaks into the dining room and kills the maid Tillie, but Peter burns it to death with a log from the fireplace. The other two maids have frozen to death before the blazing fire. The creatures from the forest mass about the doors but do not attack, and the Doctor realises that they’re here to escort the occupants of the House to a meeting. He follows the creatures to a door which only he can see, and enters the House’s cellar to confront his enemy. The others take advantage of the lull to help Bernice, who has woken in a white void where the ghost of Victoria tells her that the Assimilator will soon return her to the Matrix. She is then attacked by the steam engine which was once the Quack, but wakes just in time; Garvey, thinking for himself for the first time in his life, has used the fireplace bellows to suck the innards out of the insect and has thus been able to remove it from her throat.

Rix and his thugs follow Arthur and Aickland to Wychborn House, where Archie keeps Ace under guard while the others search the ruins. Aickland bursts out of hiding, distracting Archie, and to Aickland’s shock Ace immediately snaps Archie’s neck. When Grey finds Archie’s body he begs Rix to let them leave, but Rix shoots him and orders the others to keep searching. They manage to track down Ace and Aickland, but are frightened away by a screaming ghost -- which Ace realises is a hologram generated to keep people away from the cellar. There, she and Aickland find the dying Arthur surrounded by technological equipment from a TARDIS. Arthur gives up the last of his energy to heal Ace’s broken fingers, and vanishes into thin air. Rix, Thos and Frankie then burst in, having overcome their fear of the ghost, and in order to escape them Ace activates the TARDIS machinery…

The Quack returns to humanoid form in order to confront the Doctor, and challenges him to justify his interference. Has he never considered that his meddling may cause more problems than it solves? The Quack transforms into the steam engine once again, but before it can assimilate the Doctor, Ace and Aickland materialise in the cellar -- as do Rix, Thos and Frankie. The creature chews up the terrified Thos and spits him out again, while the others flee to the foyer. There, Ace tells her story to the Doctor, who finally realises what’s going on -- and tells her that they must leave the House at once. Rix demands an explanation, and when the Doctor momentarily hesitates, Rix shoots Peter dead -- and the violent action provokes the elemental creatures into another assault. Charlotte and Aickland flee to the roof of the House, while Rix sacrifices Frankie to the creatures to delay them while he escapes into the wine cellar. He soon realises that there is no escape, and as the creatures burst in to assimilate him, he chooses to decide his own fate and shoots himself in the head.

Garvey leads the Doctor, Ace and Benny out of the House, and gives his life to hold off the attacking elementals while the others escape into the TARDIS. Ace is furious with the Doctor for abandoning the others, but he insists that they have no choice. The House is an artificial environment, designed to embody goodness and timeless beauty, but it was not designed to cope with trespassers -- and when the Doctor and his companions arrived, the programme assumed that they were a part of it, and tried to incorporate them into its matrix. Their subconscious suspicions that evil was lurking somewhere in the environment thus became part of the programme, and as long as they remained in the House, trying to fight the evil they perceived, they were only making matters worse. The only evil in the House was that which they brought with them.

The Doctor tracks down the real location of the House to a dormant TARDIS in the asteroid belt of Earth’s solar system. Inside, he finds his old friend Galah, a Time Lady with whom he had often debated the nature of good and evil. She has placed her body in stasis and connected it to her TARDIS controls, and has channeled the surge of energy from her final regeneration into her TARDIS’ protyon units, thus creating the House and the life within. The Doctor connects himself to the protyon unit in order to rescue Aickland, only to discover that since Rix “died” before he could be assimilated, he has been able to access the code underlying the House’s environment. He has thus turned the environs of the House into a vision of Hell, and he intends to torture Charlotte and Aickland to death and use the power of the protyon units to create new life -- creatures which, like Arthur, will carry the power of the House with them into the real Universe. Unlike Arthur, they will lack the innate innocence that caused Arthur’s life energy to ebb away in the real world -- and under Rix’s guidance they will remake reality in his image.

Benny and Ace find a door in Galah’s control room which leads them into the House, and there, they try to rescue Charlote and Aickland. As they do battle with Rix’s elementals and the Doctor struggles to subdue Rix himself, Galah finally awakens to a sense of her own self, and realises that the Doctor was right all along; goodness is not a state of being, but a process. Together, she and the Doctor overpower Rix and show him what he has become; horrified by this sight of his true self, Rix offers no resistance as they erase him from the protyon core of the TARDIS. Galah explains that she built the House as a symbol of purity, modelling it on the real Wychborn House, which she had visited before the fire; however, she now accepts the Doctor’s view. Before dying, she uses the last vestiges of energy from the protyon units to preserve Charlotte; unlike Arthur, Charlotte will now be able to live an ordinary life beyond the confines of the House. The Doctor takes Charlotte and Aickland back to Earth, where they marry and Aickland begins to write ghost stories. The Doctor, Ace and Benny depart, unsure how much responsibility they bear for what happened; nevertheless, wherever he arrives, the Doctor will continue to seek out evil and fight it.