In a Victorian Gothic mansion, strange things are afoot. The master of the house, away in Egypt, has been replaced by a sinister Egyptian. Cloth-wrapped Mummies roam the grounds, killing people. Beneath a pyramid, the last of the Osirans — Sutekh the Destroyer — waits to be freed, to at long last bring his gift of death to all who live.

The New Doctor arrives on Earth in the middle of a freak meteor shower. Faceless killer shop window dummies are coming to life and killing anything that comes into their path while Facsimiles are replacing top Military, Political and Civil leaders. The Nestene has come to invade the Earth. The convalescent Doctor teams up with Brigadier Lethbridge-Stewart and Dr. Elizabeth Shaw of UNIT to thwart the Nestine's plans even as the invasion begins.

Arriving on the barren world of Androzani Minor, the Doctor and Peri find themselves embroiled in a long running, literal underground war. At the heart of the conflict is a substance called Spectrox - both valuable and deadly! The Doctor & Peri wind up being poisoned by the material, which is killing them slowly and painfully unless they can find a cure. As the conflict heats up and the situation gets more desperate, the Doctor realises time is running out - both for Peri and himself...

The Doctor answers a summons and finally returns to his homeworld, Gallifrey, seat of the Time Lords. However, when the President of the High Council is assassinated, he becomes the prime suspect, while an old enemy lurks in the shadows, pulling the strings.

The TARDIS arrives on Earth in the middle of a meteorite shower and the Doctor is found by UNIT troops and taken to a nearby hospital. The Brigadier is faced with having to cope not only with the mysterious meteorites but also with Ransome, an ex-employee of a local plastics factory, who claims he has seen a walking mannequin. The meteorites turn out to be hollow globes containing the Nestene consciousness, a disembodied alien intelligence with an affinity for plastic. A Nestene agent, Channing, has infiltrated the plastics factory and is using energy from the globes to animate Autons - mannequin-like figures and realistic replicas of senior establishment figures - with the aim of colonising the Earth. Aided by newly-recruited UNIT scientist Dr Elizabeth Shaw, the Doctor thwarts this scheme by repelling the Nestene consciousness into space and thereby neutralising the Autons and the monstrous tentacled form that it has been creating for itself in a tank within the factory. Channing, revealed to be no more than a sophisticated Auton, is likewise deactivated.

Arriving in London at the end of the 19th Century, the Doctor and Leela make friends with a police pathologist, Professor Litefoot, and learn that hairs taken from the clothing of a dead body found floating in the Thames seem to have originated from a very large rat. The Doctor's investigations take him first to the sewers, where there are indeed giant rats on the loose, and then to the Palace Theatre, where a stage magician, Li H'sen Chang, is procuring young girls for his master, the ancient Chinese god Weng-Chiang. Weng-Chiang is in fact Magnus Greel, a war criminal from the 51st Century. The journey back through time has disrupted his molecular structure and he now needs to feed on the life force of others - hence his use for the young girls. He has come to London to retrieve his lost time cabinet, which is in the possession of Litefoot. Infiltrating Litefoot's home with Chang's ventriloquist doll Mr Sin - a computerised homonculus with the brain of a pig - he retrieves the cabinet and prepares to travel back to his own time. The Doctor, aided by Leela, Litefoot and Henry Gordon Jago, the proprietor of the Theatre, tracks him down to his lair and traps him before he can escape. Greel falls into his life force extraction machine and disintegrates. The Doctor is then attacked by Mr Sin but manages to disconnect its circuitry, rendering it inanimate.

The TARDIS arrives on an apparently deserted and deactivated space station Nerva, otherwise known as the Ark, orbiting Earth in the far future. There the Doctor, Sarah and Harry discover the last survivors of the human race held in suspended animation, Earth having been evacuated thousands of years earlier when solar flares threatened to destroy all life. The station has been visited by a Wirrn, an insect life form, which has laid its eggs in the solar stacks and absorbed the body and mind of one of the sleeping humans. The Doctor's reactivation of the station's systems causes the humans to start to revive. Their leader, nicknamed Noah, becomes infected by one of the emerging larvae and is slowly taken over. The Doctor and his friends meanwhile gain the trust of the other humans, now led by a med-tech named Vira. Together they manage to lure the hatched Wirrn insects into a shuttle craft and then eject it into space. In a final act of humanity, Noah - by this time fully transformed into a Wirrn - deliberately neglects to set the shuttle's stabilisers, causing it to explode.