The TARDIS takes the newly regenerated Doctor to Earth to begin his exile. Brigadier Lethbridge-Stewart leads a UNIT investigation into a mysterious meteorite shower.
A recovered Doctor escapes the hospital and joins UNIT in their investigation. Meanwhile, Channing directs one of his Auton servants to recover a meteorite.
Sam Seeley has found one of the meteorites but the Autons want it back and are closing in. General Scobie visits Auto Plastics, playing into the hands of Channing.
The invasion begins as Auton shop dummies come to life and attack the public. The Doctor and UNIT infiltrate Auto Plastics where the Doctor faces the Nestene consciousness.
UNIT are summoned to Wenley Moor research station which is experiencing mysterious power losses. In the nearby caves, one of the staff has been killed and another sent insane.
Investigating the caves, the Doctor is attacked by a dinosaur-like creature. Dr Quinn is hiding a secret that could endanger the lives of everyone.
The creature from the caves, wounded and dangerous, is on the loose on Wenley Moor. Dr Quinn attempts to recover it and is unwilling to listen to the Doctor's warnings.
Fearful of a war breaking out between the Silurians and mankind, the Doctor attempts to make peace between the races. But there are those on both sides unwilling to listen.
As the Silurian plague quickly spreads, the Doctor desperately searches for a cure. But the Silurians are aware of the Doctor's efforts and intend to stop him.
With the antidote to the plague found, the Silurians retaliate and take over the research centre. They now intend to destroy the Van Allen Belt, resulting in death for all mankind.
Contact has been lost with Mars Probe 7. When contact is also lost with the recovery ship, UNIT is called in and the Doctor learns that someone is sending messages to the vessel.
Recovery 7 has returned to Earth but the UNIT convoy transporting the capsule is ambushed. The Doctor is able to relocate the capsule, but is he too late?
The recovery capsule is empty with the astronauts seemingly kidnapped. But Liz notices that the radiation count is high and the Doctor deduces that the occupants were not human.
Liz has been captured by Reegan who is holding the three aliens captive. The Doctor suspects Quinlan's part in the conspiracy, but Quinlan is killed before he can reveal the truth.
The Doctor prepares to pilot the Recovery 7 ship into space, but Reegan sabotages the fuel supply which will send the Doctor into the sun.
On board a vast spacecraft, the Doctor meets the alien captain who demands the return of the three ambassadors sent to Earth or he will destroy the world.
General Carrington is behind the kidnapping of the ambassadors and intends to turn the world against the aliens by revealing their true identity to the world in a TV broadcast.
UNIT are at a project run by Professor Stahlman who plans to penetrate Earth's crust. But the drilling has already released something deadly from beneath the planet's surface.
The green slime oozing from the drill head is transforming men into monsters. Stahlman refuses to listen to the warnings and resorts to sabotage so that his project may continue.
Transported to a parallel world, the Doctor discovers that England is under military rule and the drilling project is at a more advanced stage.