The Doctor, having had his regeneration forced by the Time Lords, has been exiled to Earth. The Doctor collapses outside his TARDIS and is taken to a local hospital where his unusual anatomy confounds doctors.
Concurrent with the Doctor's arrival, a swarm of meteorites falls on the English countryside, and a poacher discovers a mysterious plastic polyhedron at the crash site. In the meantime, Brigadier Lethbridge-Stewart of UNIT is trying to recruit Dr. Elizabeth "Liz" Shaw as his scientific advisor and investigate the unusual meteorite falls. Shaw, however, is sceptical of the Brigadier's claims of alien invasion and is resentful of being taken away from her research at Cambridge. Soon, the Brigadier is faced with another mystery; not far from where the meteorite impacts were reported, a man in hospital claims to be the Doctor (whom Lethbridge-Stewart last encountered in The Invasion). However this Doctor looks nothing like the Doctor the Brigadier knew.
The plastic polyhedron is actually a power unit for a non-physical alien intelligence known as the Nestene Consciousness. Normally disembodied, it has an affinity for plastic, and is able to animate humanoid facsimiles made from that material, known as Autons. The Nestene have taken over a toy factory in London, and plan to replace key government and public figures with Auton duplicates. The Auton in charge of the factory sends other, less human-looking Autons to retrieve the power units from UNIT and the poacher.
After a failed attempt at escaping from the hospital (which results in him nearly being shot dead by an overzealous UNIT trooper), the Doctor discovers that his TARDIS has been disabled by the Time Lords and he is trapped on Earth. He convinces Lethbridge-Stewart that he is the same man who aided him before to defeat the Yeti and the Cybermen, despite his change in appearance. Together with Liz, he uncovers the Nestene plot, just as Auton mannequins are activated across Britain and start killing people. However, the Doctor creates an electroshock device that he believes will disable the Autons.
UNIT attacks the plastics factory, but the Autons are impervious to gunfire. The Doctor and Liz make their way inside and encounter the octopus-like plastic creature that the Nestenes have created with the power units as the perfect form for the invasion. While the Doctor struggles with the creature, Liz manages to use his machine to shut the creature down, and all the Autons "die" as well, being part of the Nestene gestalt consciousness.
The Brigadier fears the Nestenes will return and asks for the Doctor's help. The Doctor agrees to join UNIT in exchange for facilities to help repair the TARDIS and a car like the sporty antique roadster he commandeered during the adventure. At his insistence, Liz stays on as his assistant.