In Yorkshire in 1893, reporter Edmund Thursday breaks into the Sweetville private community. He and his fellow reporter Effie make their way a strange room with a glowing red light shining through the window, and Edmund tells her to go to the police if he doesn't return in an hour. As he goes in, Mrs. Winifred Gillyflower and several of her staff come up behind Effie. Mrs. Gillyflowers expresses her condolences to Effie about Edmund's death. When Effie points out that Edmund isn't dead, a ghastly scream echoes out of the red room. Mrs. Gillyflower and her people advance on Effie, who screams in terror.
Later, Edmund's corpse turns up in the canal and is delivered to the local coroner, Amos. Edmund's twin brother, Mr. Thursday, comes to pick it up and is shocked to discover that the skin is petrified solid and a bright shade of red. Amos says that other corpses have turned up that way, and that Mrs. Gillyflower doesn't want word leaking out.
Mr. Thursday returns to London and calls on the famed private investigator, Madame Vastra. He speaks with the veiled woman and her maid, Jenny, and explains that his brother was working undercover with Effie to find out what Mrs. Gillyflower was doing. Mr. Thursday shows Vastra a photo that he took of his dead brother's eyes, hoping to reveal the last thing he saw. Vastra dismisses it as superstition until she discovers that there is an image in the eye. She removes her veil to get a better look and Mr. Thursday faints at the sight of her Silurian features. Vastra and Jenny develop the other photos and discover that the last thing Edmund saw before he died was the Doctor.
Vastra, Jenny, and Strax travel to Yorkshire and go over their plan. Since Mrs. Gillyflower only wants the brightest and most people in her community, Jenny will go to a recruitment meeting. At the meeting, Mrs. Gillyflower gives a sermon about the world's moral decay and the coming apocalypse that will rain down on everyone. She then reveals her daughter, Ada, who is blind due to hideous red scars on her face. Mrs. Gillyflower explains that her husband beat Ada in a drunken rage, blinding her, and invites those who are suitable to join Sweetville. Jenny approaches with the others and Mrs. Gillyflower assures her that she is suitable. Outside, Vastra and Strax wait for Jenny to investigate and find the Doctor.
The next day, Ada goes to the upper floor of the factory with a plate of food. She takes it to a locked cell door and slides it through the slot at the bottom. As she does so, Ada whispers to the creature inside, saying that she hasn't forgotten "her monster."
Mr. Thursday returns to Vastra's home to get an update, but faints when Strax answers the door. Strax drags him inside and tries to wake him up, while Vastra assumes that he's there to check on the progress of the investigation.
Jenny stands in the recruitment line and talks with the person next to her, Abigail. Abigail admits that she had a friend who joined the Sweetville community three months ago, but hasn't been seen since. Jenny notices a nearby locked door and pays Abigail a guinea to fake a faint as a diversion. Once Abigail does so, Jenny slips away and goes to the main factory. She discovers that the room is empty except for giant gramophones playing the sounds of factory machinery. Several of the Sweetville workers pass by, carrying large jars of a red fluid, and Jenny follows them.
Vastra goes to the Yorkshire morgue and meets with Amos, who gives her some of the crimson fluid he's taken from the corpses. The Silurian looks at it and is surprised to discover that she recognizes it... from 65 million years ago.
At dinner, Mrs. Gillyflower and Ada eat and Ada wonders if Mr. Sweet will ever join them. Mrs. Gillyflower says that her partner is feeling tired and spills some salt. She dismisses the servant and then, sure that her daughter can't see what she's doing, pours some of the salt down her blouse.
Jenny makes her way to the red room, but hears a noise upstairs. She goes up and hears something banging on the cell door. When she opens the feeding slot, the monster inside reaches a scarlet-colored hand out. Jenny slams it shut and then tells the creature that she's there to help it. It bangs out a positive response and Jenny confirms that it is saying it won't attack her. She then picks the lock on the door and goes inside... and finds the Doctor, his skin a bright shade of red. HIs skin is petrified, preventing him from speaking or moving very easily.
Once she's freed him from his manacles, Jenny leads the Doctor out. When Ada comes out of the elevator, Jenny takes the Doctor into the red room. Inside is a large vat of red fluid and a suspended rack of new Sweetville resident. The staff lower the newcomers into the fluid, submerging them, and Jenny realizes that the same thing happened to the Doctor. He manages to point down a hallway and Jenny leads him down the corridor.
Ada goes to the cell and discovers that her monster is gone.
The Doctor leads Ada to a coffin- metal chamber and activates it with his sonic screwdriver, and then goes inside. The light inside turns green and the mechanism restores the Doctor to normal. He immediately runs off, saying he needs to find Clara, and Jenny wonders what he means since she saw Clara die in Victorian London. The Doctor calls out an explanation as he goes.
The Doctor and Clara arrive in Yorkshire and immediately hear a woman's scream. They run to investigate and discover that the woman saw a corpse floating in the canal. Edmund is there, insisting that someone has to listen to him. The Doctor takes him up on his offer and Edmund tells him that Mrs. Gillyflower owns the local match factory and is a talented engineer and chemist. However, no one who goes to work at the factory never leaves. They go to the morgue to examine the corpse, and the Doctor confirms that the eye could capture the last image it saw, if something had corrupted the body's chemical composition. He then analyzes the red liquid and confirms that it's an organic poison.
Edmund insists that they need to come up with a plan and the Doctor and Clara are soon applying for residency at Sweetville, claiming to be husband and wife. Mrs. Gillyflower shows them around and explains that the community is named after her silent partner, Mr. Sweet. The older woman takes them to an apartment and shows them two of the residents: in suspended animation inside a giant bell jar. Sweetville guards take the Doctor and Clara to the vats and submerge them in the red liquid. Clara is rendered mindless and petrified, but the Doctor's skin turns bright red: a side effect of the transformation process. Mrs. Gillyflower orders him thrown in the canal with the other rejects, but Ada takes a fancy to him and hides him away. She explains that Mr. Sweet is the only one who understands the process and that the Doctor is the first one to have been rejected but survived. Ada tells the mute Doctor that she'll keep him in the cell as her special monster. Sometime later after she leaves, Edmund bursts into the cell and finds the Doctor. The reporter's skin is bright red and he dies, the Doctor's face the last thing he sees.
The Doctor tells Jenny that Mrs. Gillyflower has been using the venom to "preserve" people for the coming apocalypse that she's predicting. When she mentions Mrs. Gillyflower's words about "raining down," the Doctor takes an interest. He then runs off to find Clara, only telling Jenny that Clara's survival is "complicated."
Strax takes a carriage back to Sweetville but gets lost along the boy. A young urchin, Thomas Thomas, offers him directions and Strax takes the boy along with him.
Jenny continues to ask the Doctor about Clara and he continues to avoid answering. He finally locates the apartment where Clara is kept under glass and breaks the giant bell jar.
Ada clutches at the Doctor's manacles, sobbing, and Mrs. Gillyflower finds her there. Her daughter admits that she formed a sentimental attraction to one of the rejects, and Mrs. Gillyflower realizes that she has to accelerate her plans for the Great Work before the outside world discovers what she's doing. Ada begs her mother to take her into her New Eden, but Mrs. Gillyflower says that she and Mr. Sweet will only settle for perfection.
The Doctor takes Clara to the metal chamber he used earlier and tries to reverse the process on her. The Sweetville guards arrive and Jenny tells the Doctor to stand back while she fights them. However, they quickly outnumber her but Strax arrives in time to open fire and drive them off. Vastra comes in behind her and Jenny tells her about Clara. The Doctor avoids Vastra's questions about how Clara can be alive, just as Clara revives. As Vastra and Jenny stare at the woman they saw die, the Doctor tells them that Clara isn't who they think she is.
As they leave the red room, Vastra explains that the Crimson Horror is a leech that the Silurians dealt with when they ruled the planet, 65 million years ago. The creature infested their drinking water and released a toxic poison. As the Doctor tires to work out what Mrs. Gillyflower is doing, Clara finally manages to get his attention and point out that the chimneys are producing smoke, but there's no factory machinery. They investigate further and discover that Mrs. Gillyflower has built a missile in the largest chimney, and her people are preparing to load it with the Crimson Horror. The Doctor tells Vastra and Jenny that he has plan.
The Doctor and Clara go back to the red room and find Ada, crying on the floor. When she feels his face, Ada realizes that the Doctor is her monster, now cured. She insists that she's not chosen and that the darkness comes from within her. When the Doctor asks her who Mr. Sweet is, Ada refuses to betray her mother. The Doctor tells her that she needs to come with them because there's something she needs to know.
Vastra and Jenny approach the large bottle holding the Crimson Horror liquid.
The Doctor and Clara burst into Mrs. Gillyflower's room as she prepares to launch the missile from a console hidden behind a pipe organ. When the Doctor asks to see Mr. Sweet, Mrs. Gillyflower tells him that her silent partner is close and unbuttons her blouse. The parasite is attached to her chest, feeding on her blood. Mrs. Gillyflower tells them that the parasite was living in the river when she found it, feeding on the pollutants. The Doctor warns her that the venom could wipe out the entire population and Mrs. Gillyflower, well aware of that, says that has been her plan all along.
Outside, Strax and Thomas watch as the central chimney lights up.
Mrs. Gillyflower explains that the venom will rain down out of the clouds, killing most of the world's population. Then she will release her specimens from suspended animation and use them to repopulate the planet. The Doctor asks about Ada and Mrs. Gillyflower dismisses her daughter as inconsequential because of her corruption. The Time Lord points out that the red scarring on Ada's face indicates that Mrs. Gillyflower caused the damage herself, and the older woman admits that she used Ada as a guinea pig to create an anti-toxin for herself. Ada, who has been standing outside, hears her mother's confession and lashes out at her with a cane. Meanwhile, the Doctor prepares to use his sonic screwdriver to destroy the launch mechanism but Clara smashes it with a chair.
Shocked at the turn of events, Mrs. Gillyflower cries and asks Ada to come to her. However, she then grabs her daughter and holds her hostage with a pistol. She ducks out the door and locks it behind her, dragging Ada with her. The Doctor and Clara jump out the window and run to the central chimney. Mrs. Gillyflower ascends the stairs to the top, dragging Ada with her, and reaches the secondary launch control. Ada pulls away and falls to the next landing, and begs her mother to shoot her and finish the job she started. The Doctor pulls the woman away while Mrs. Gillyflower launches the rocket and laughs in triumph.
As the missile soars up into the sky, Vastra and Jenny arrive... carrying the Crimson Horror that was intended to go into the missile. Realizing that she's been foiled, Mrs. Gillyflower prepares to shoot them but Strax calls down from the top of the chimney. He orders her to surrender but she fires at him and he fires back. A stray shot hits her hand, knocking her over the railing. She falls to the floor several stories below and lies crushed. The others run down and see Mr. Sweet crawling away from his now useless host. Mrs. Gillyflower begs Ada for her forgiveness, but Ada refuses and her smiles in satisfaction. As she dies, the Doctor suggests taking the leech back in the TARDIS. Ada makes the matter moot by crushing it with her cane in a fit of anger.
The next day, the Doctor and Clara go to the TARDIS and the others say their goodbyes. Ada tells the Doctor that she plans to go out into the light. The Doctor assures her that she'll be splendid and says goodbye to the others. Jenny asks about Clara and says that he hasn't explained, and the Doctor agrees. He goes into the TARDIS and it departs just as Mr. Thursday arrives, sees it, and faint.
The Doctor returns Clara home and departs, and she discovers that Angie and Augie Maitland have been checking the Internet and have photos of Clara up on their computer. There are photos of her in the 1980s and 1970s, and they come in and ask if the Doctor is Clara's boyfriend. Angie shows Clara a third photo showing her in Victorian London, where Clara has never been. Before Clara can pursue the matter, the kids ask if they can go with her the next time she travels through time. Clara refuses until they tell her that they'll tell their father if she doesn't.