London, 1894. Factory owner Nathaniel Seers, formerly one of the kindest of men, has recently changed for the worse. When his loyal employee Tom Donahue’s hand is crushed in an accident, Seers accuses him of carelessness and fires him. Seers’ family has fared little better, and when his daughter Emmaline finds her mother in tears after a confrontation with her father, she vows to confront him and discover what has changed him so. Seers, meanwhile, is involved in shady dealings with criminals Jack Howe and Albert Rudge, who are supplying him with fresh corpses for reasons he does not choose to reveal to them; Howe, however, intends to follow his mysterious employer one night, find out what he is really doing and use the information to blackmail him. Meanwhile, Donahue is unable to find work and is suffering from gangrene in his crushed hand. Desperate to avoid the workhouse, he returns to the factory after hours to beg Seers to take him back -- only to find Seers chopping up body parts in a disused shed as his eyes glow bright orange.
The Doctor accidentally destroys one of his collected back issues of the Strand magazine, and takes Sam to Victorian London to buy another copy. The TARDIS materializes on a towpath on the Thames in the middle of the night, and as the Doctor and Sam attempt to get their bearings they run into Donahue, who is fleeing in terror from the devil he saw at the factory. Donahue flees into the mist, and moments later the Doctor and Sam hear a terrible scream -- and see a dinosaur-like figure retreating into the Thames. They report the incident to the police -- as much as they feel will be believed -- and when pressed to give his address, the Doctor claims to be staying with his old friend, pathologist George Litefoot. When the Doctor shows up in his eighth instead of his fourth body, Litefoot has no idea who he is at first, but the Doctor claims to be an associate of the “other Doctor”, and enlists Litefoot’s aid in his investigation. Litefoot is only too glad to assist him, especially when the body of Tom Donahue is pulled out of the Thames, having been bitten in half by an enormous creature.
The Doctor sets off to investigate the dead man’s former place of employment, but Seers is obstructive and unhelpful, and seems to be hiding something about the factory cellar. Emmaline attempts to confront her father about his behaviour but is also sent away frustrated; the Doctor, however, observes her demeanour and asks her to contact him should she learn anything further about her father’s changed behaviour. Seers’ suspicions have been aroused, however, and he determines to investigate this strange Doctor who seems to know more than he should. Later that night, with the reluctant assistance of Professor Litefoot, the Doctor and Sam break into the factory to learn more. They discover a hidden door in the cellar, protected by an organic lock -- and are then attacked by a monstrous beast which has been augmented with cybernetic implants. The Doctor uses his sonic screwdriver to drive off the beast while they make their escape, but he has confirmed that the forces at work here are alien.
Emmaline is woken by the sounds of a struggle, and when she investigates she finds her mother dead and her father standing over the body, his eyes glowing orange and venomous stings protruding from his hands. The Doctor, Sam, and Litefoot are discussing their next move at Litefoot’s home when Emmaline arrives, having fled from her house in terror. The Doctor, theorizing that the creature in the factory will now have been let loose to roam the grounds, decides to break back in through the sewers, and Emmaline insists upon accompanying them to find out what manner of being has possessed her father. The Doctor leads the party through the sewers into the cellar, where he uses his sonic screwdriver to open the organic lock and thus reveals a passageway which appears unpleasantly like an enormous living creature’s feeding tube. He and his companions pass through the tube to find themselves in a living spacecraft, and when they finally spot the occupants the Doctor recognizes them as Zygons. The smell of putrefaction is explained when the Doctor finds a chamber of Skarasen feeding on human remains, and when he also finds a set of incubator tanks he concludes that the Zygons are preparing for invasion.
Before the Doctor can investigate further, Emmaline transforms into a Zygon and turns them in; the real Emmaline never escaped from her parents’ house. Sam and Litefoot are placed in the body-print machinery and duplicated, but the Doctor is able to resist the process. Enough of his memories are analysed, however, to reveal to the Zygon warlord Balaak that the Doctor possesses a time machine. The Doctor is placed in the custody of the scientist Tuval, and is ordered to take her to the TARDIS; if he attempts to harm her in any way, the disruption to her neural patterns will be detected, and Sam and Litefoot will be killed at once. Tuval takes on Sam’s form, and as the Doctor takes her to the TARDIS, Tuval explains that the Zygon ship was damaged in a battle with their enemies the Xaranthi and crashed on this planet some years ago. Balaak has been breeding an army of Skarasen in order to wipe out the human race and create a new home for the Zygons. The Doctor offers to take the Zygons to an uninhabited world, but as much as Tuval would prefer to avoid bloodshed, she knows that once Balaak has set a plan in motion he will not abandon it; the human race is as good as doomed. The Doctor lets Tuval into the TARDIS and starts to show her how to operate the control console, but while doing so he traps her in a temporal loop, causing her to repeat the same ten seconds of time over and over again -- thus keeping her imprisoned without disrupting her neural patterns.
While Balaak is otherwise occupied, another Zygon takes the form of Litefoot and meets Howe and Rudge to collect the bodies with which the Zygons have been feeding their Skarasen army. However, this time Howe and the reluctant Rudge to follow their mysterious benefactor, and once he arrives at Seers’ factory they confront and attempt to blackmail him. The infuriated Zygon drops his disguise and stings Rudge to death, and the terrified Howe stabs the alien creature to death and flees while the Skarasen “watchdog” is consuming Rudge’s body. Litefoot is released by the body-print machinery at the moment of his duplicate’s death, and he manages to escape before the Zygons realize what has happened; however, he emerges from the ship underwater, and the effort of reaching the bank of the river causes him to lose consciousness. A passing constable recognizes him and takes him to the nearest hospital to recover. Meanwhile, Howe flees to a nearby gin palace, where he tells his story and cuts out the tongue of a man who was foolish enough to dispute him. Convinced that the devil has made his home in the factory, Howe whips up the patrons of the gin palace into an angry mob and takes them to torch the factory. The Zygons, realizing that their cover has been exposed, decide to move their spaceship.
The Doctor, trying to swim back to the ship, is nearly crushed when it begins to move, but he manages to avoid the moving legs and re-enter the ship. Inside, he finds the vats of Skarasen lactic fluid, which the Zygons need to consume at regular intervals, and slips an anesthetic into the supply. He then rescues Sam from the body-print machinery and takes her back to the TARDIS, where he frees Tuval and explains what he has done. Once the Zygons are all asleep he will programme their ship’s autopilot to take them to an unhabited world, and delete all record of Earth’s location from its databanks to ensure that Balaak will never be able to return. Tuval accepts the Doctor’s plan as suitable -- but when the Doctor takes the TARDIS back to the Zygon ship, he discovers to his horror that he has miscalculated and that the anaesthetic has killed every Zygon aboard the ship. The dying Balaak stings the Doctor, operates the ship’s self-destruct unit, and, in a final act of spite, releases the Skarasen to wreak havoc in the world above. He then enters the TARDIS with Tuval and orders her to pilot them to a place of safety, but the Doctor has pre-programmed it to take them to the riverbank. Litefoot has returned in search of the Doctor and Sam, and when Balaak emerges from the TARDIS and attacks him Litefoot shoots him dead. Tuval refrains from attacking Litefoot in turn, however, telling him that there has been too much death already -- and that there will be more to come.
The Doctor recovers, as Balaak was too weak to apply a fatal sting; however, despite Sam’s insistence, he is unable to go back in time to undo the wrong he has done, as it is impossible to change an event which has already occurred. He releases the Zygons’ prisoners, including Nathaniel and Emmaline Seers, and explains the situation; despite their terror at their unfamiliar surroundings, the captives accept the need for urgency and agree to follow the Doctor’s instructions. The Doctor is thus able to slow down the ship’s self-destruct sequence long enough to pilot the ship to the riverbank, and he and the others escape moments before the ship explodes. The Skarasen are already loose in London, however, spreading terror and destruction, and killing and eating everyone they encounter, including Jack Howe. The Doctor urges the others to find a safe place to hide, while Sam and the Seers accompany him back to the TARDIS, which he realizes will have materialized back where he left it. After a dangerous journey through the Skarasen-infested streets, they reach the TARDIS, where the Doctor and Tuval programme the TARDIS console to genreate a signal that will lure the Skarasen to it. The Skarasen are thus drawn back to the TARDIS, lulled back into dormancy. The Doctor then sends Litefoot and the Seers to safety and uses the TARDIS to pilot Tuval and the dormant Skarasen to an uninhabited world, where they can start a new life.