Gabriel Chase, a Victorian mansion in Perivale. Reverend Ernest Matthews, Dean of Mortarhouse College, Oxford, arrives for dinner to challenge the blasphemous theories of the house's owner, Josiah Samuel Smith; the day housekeeper, Mrs Grose, shows him to the drawing room and then flees the house in terror, as it's closing in on six o'clock and nobody in their right minds stays in the house after dark...

The TARDIS materializes in the upper observatory of the house. Ace finds the surroundings creepy and hopes the Doctor hasn't brought her to a haunted house; one bad experience was enough for her. She and the Doctor explore the upper floors and find a radioactive snuffbox, and are confronted by an oddly intense explorer who identifies the snuffbox as the property of Redvers Fenn-Cooper, a man who vanished mysteriously while visiting Josiah Samuel Smith. The explorer turns out to be Redvers himself, who has been driven mad by his exposure to some kind of "light". The night housekeeper, Mrs Pritchard, takes Redvers back into the heart of the house for treatment, while a Neanderthal butler Nimrod shows the Doctor and Ace to the drawing room. The Doctor hands Nimrod the fang of a cave bear, a token of wisdom amongst the elders of Nimrod's tribe, and Smith, puzzled, orders Nimrod to the cellar to carry out his duties there. But Nimrod is attacked and knocked out by the creature which Smith keeps locked up in the cellar.

While Smith's ward Gwendoline shows Ace to her room to find suitable clothing, the Doctor and Matthews speak with Smith, whose treatises on Darwin's theories of evolution have provoked outrage amongst the God-fearing Victorians. Their discussion is interrupted by the sound of Redvers screaming, and the Doctor investigates to find that Redvers' snuffbox is glowing with a harsh white light which Redvers seems terrified of. Ace and Gwendoline, both dressed in mens' clothing, join the Doctor and Matthews at dinner, but Matthews' attempt to pontificate is interrupted by the sound of a telephone ringing. Smith answers the telephone and hears the voice of his captive from the cellar -- it's learned how to speak. Smith has Mrs Pritchard knock Matthews out with a chloroformed handkerchief, planning to continue their discussion later.

The Doctor offers his help, hoping to find out what's going on, but he is angrily confronted by Ace, who's learned that this house is the same haunted house she once told the Doctor she never wanted to return to. The Doctor has brought her back to force her to confront her own fear and to satisfy his own curiosity -- he's convinced that the evil force Ace sensed in the ruins of the house as a young girl is alien in origin. Ace admits that she entered the house on the worst day of her life, the day her friend Manisha's flat was firebombed by racist white kids, but before she can tell the Doctor what happened next Smith arrives to ask the Doctor for help, and Ace's nerve breaks and she flees.

The Doctor discovers that, in addition to the stuffed animals in his collection, Smith also has a human specimen -- police inspector Mackenzie, hypnotised and preserved in a collection drawer. Gwendoline is also under Smith's hypnotic control and believes that Mackenzie is a rare insect from Java; her own father "went to Java" after seeing what Smith was keeping in the cellar. Smith orders the Doctor to help him and threatens dire consequences should he refuse. Meanwhile, Nimrod recovers and saves Ace from the attacking husks, but when Ace threatens to smash a glowing membrane which the husks seem to be avoiding, Nimrod tries to stop her and accidentally stumbles against the membrane, disturbing the thing inside.

The resulting energy release is detected in the house, and while Smith is distracted the Doctor holds a radiation detector to his head, pretending it's a gun, and forces Smith to take him to the cellar. There, Smith orders the Doctor and Ace to help him stabilise the energy release, and the Doctor realizes that the "cellar" is in fact a stone spacecraft -- and Smith isn't the owner, but part of the cargo. He manages to stabilise the energy release and save England from destruction, but the creature controlling the husks then attacks them, and they retreat back to the lift with Nimrod.

The Doctor wonders whether the creature is the depraved monstrosity Smith claims it to be, but has no time to investigate; it's nearly daylight, and Smith destroys the lift and retreats to the upper observatory, shedding his skin. Ace, exhausted, falls asleep in the drawing room as Gwendoline follows Smith to the upper observatory. There, Smith awakens Matthews and causes him to transform into an ape whilst he denounces Darwin's theories of evolution. Smith soon tires of his new toy and hands Gwendoline a chloroformed handkerchief, ordering her to send Matthews to Java.

Ace awakens to find that it's nearly evening, and while she's been asleep the Doctor has been busy. He's awoken Mackenzie to provide himself with help investigating, but finds Mackenzie's mind utterly methodical and closed to the unusual. He and Ace awaken Nimrod, who recites legends of his tribe and announces that the Burning One, Light, will soon return. Ace discovers that while she was asleep the Doctor repaired the lift and made a deal with "Control", the creature from the cellar, to awaken Light; he suspects that Light is the true owner of the ship and wants to speak with it about what's been going on while it slept.

Light takes the form of an angel, and the Doctor explains to Ace and Mackenzie that it's on a mission to catalogue all forms of life in the Universe. Josiah is its survey agent, capable of evolving to mimic the native forms of life in any environment; Control is linked to the Survey Agent to prevent it from evolving too far and breaking free of Light. But while Light slept the Survey got out of Control. Light can't believe that this planet is Earth; it's changed so much since he surveyed it that his survey of the planet's life forms is out of date. He dissects one of the maids to find out how she works, and eventually realizes that this is indeed Earth -- and that due to evolution, his painstaking research has been wasted. Furious, he selects Mackenzie to start the change back.

Control, exposed to the upstairs environment, begins evolving into a beautiful young woman, but her personality remains largely instinctive and animal-like. The Doctor seeks her help in dealing with the situation but she flees from him, fearing he will take her newfound freedom away. While puzzling out his next move, the Doctor happens across Fenn-Cooper, who reveals that he's on a big game hunt funded by Smith -- to hunt the rarest animal of them all, the "Crowned Saxe-Coburg". Fenn-Cooper has a personal invitation to Buckingham Palace, and the Doctor realizes that Smith intends that Fenn-Cooper should assassinate Queen Victoria so Smith can rule the empire in her place.

Smith sends Gwendoline to dispose of Ace, but Ace overpowers her and flees to find Control huddled in a bedroom, terrified of the big open empty world outside the house. Ace urges Control to keep evolving and beat Josiah at his own game, and Control improves her diction and bearing, becoming a young lady. The Doctor and Fenn-Cooper arrive just in time to save Ace from Gwendoline, and the Doctor shows Gwendoline a cameo of herself and her mother, Mrs Pritchard. Gwendoline freezes in shock upon realizing what she has become. The Doctor then reveals the truth to Mrs Pritchard, sending her in tears to her daughter's side -- but Light, accusing them of "adapting to their situation to survive", kills them both, calcifying them in stone so they'll never change again.

The Doctor, Ace, Control and Fenn-Cooper go to dinner, where the Doctor reveals Smith's plans. Fenn-Cooper then offers his invitation to Control rather than Smith, ruining Smith's plans, and when Smith confronts Control she threatens to burn down the house. Ace is horrified and reveals that that's exactly what she did, in 1983, instinctively acting to erase the evil she sensed here. Control tosses the invitation into the fireplace, finishing Smith's plans.

But there's still Light to take care of. He's transformed Mackenzie into primordial soup as a prelude to his plans for Earth; to ensure that his catalogue remains up to date, he has programmed his ship to explode and eradicate all life on the planet. But the Doctor points out that Light too changes and evolves -- his shape, his attitudes, his location. Nimrod refuses to continue serving Light, pledging his allegiance to his planet; even Control has evolved beyond Light's control. Unable to cope with the rapid changes, Light calcifies himself.