In 1893 Yorkshire, bodies are being washed up all bright red and waxy in the river of a mill town. While a man identifies the body of his brother, an optogram reveals an image preserved on the dead man’s eye – the Doctor. After learning of this, Silurian sleuth Madame Vastra (Neve McIntosh), her wife Jenny (Catrin Stewart) and Sontaran butler Strax (Dan Starkey), decide to investigate.
At a local community hall, Mrs Gillyflower (Diana Rigg) is running a recruitment drive to attract healthy, good looking young pilgrims to move into Sweetville, a mill turned model village that she has created (along with her unseen silent partner Mr Sweet) as a utopian alternative to the moral decay of cities that have caused much ugliness in the world, and resulted in the disfigurement and blinding of her own daughter Ada (Rachael Stirling).
Unbeknownst to Mrs Gillyflower, Ada has a victim of the Crimson Horror locked up inside the mill. While going undercover, Jenny discovers the victim is the Doctor, who uses his sonic screwdriver to undo the effects of the strange affliction. Flashbacks then show the Doctor and Clara being captured by Mrs Gillyflower – who plans on preserving her pilgrims against an Apocalypse that she and Mr Sweet have designed – and being dipped into a vat containing the mysterious substance, which works on Clara, but fails on the Doctor.
Back in the present, Jenny is bemused by the Doctor’s reference to Clara, who died a year ago, but is astounded when he locates Clara inside a giant bell jar and revives her. Analysing the liquid, Vastra discovers it is, in fact, a parasite that almost wiped out her own kind, the Silurians. Clara then deduces that Mrs Gillyflower plans to launch a missile inside a chimney that isn’t blowing smoke to release the poison.
When Ada refuses to give up the identity of Mr Sweet, the Doctor confronts Mrs Gillyflower, who reveals he is actually a creature that is attached to her own body. Together they envisaged a golden dawn for humanity, where no imperfections would be allowed. Mrs Gillyflower then admits that she used Ada as a human guinea pig to produce an anti-toxin to save herself. Feeling betrayed, Ada attacks her mother, while Clara destroys the missile’s controls. Mrs Gillyflower then heads to a secondary firing mechanism and launches the missile – but Vastra and Jenny have offloaded the poison. As Mrs Gillyflower opens fire, Strax shoots from above, causing her to fall. Mr Sweet then crawls away from her body and is crushed under Ada’s cane.
Back at the Tardis, the Doctor bids goodbye to Ada and his friends, but refuses to explain more about Clara. Returning home to present day London, Clara discovers her charges have found evidence of her time-travelling antics and blackmail her into accompanying her on her next adventure…