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.

Investigating mysterious power failures and a death at an underground research centre, The Doctor discovers a colony of Silurians - prehistoric, intelligent reptiles who went into hibernation before man evolved. But now they have woken up, and they are prepared to wipe out mankind with a killer plague to get their planet back.

Astronauts rescued from a mission to mars are kidnapped when they arrive back on earth. They seem to have been irradiated, and can now kill people merely by touching them. But the Doctor discovers the astronauts have been replaced with Alien ambassadors who are being forced to behave in a hostile manner. With The Doctor traveling to the alien mother ship, and Liz kidnapped, The Brigadier is left wondering who to trust.

UNIT is providing security cover at an experimental drilling project at Eastchester, designed to penetrate the Earth's crust and release a previously untapped source of energy. Soon, however, the drill head starts to leak an oily green liquid that transforms those who touch it into vicious primeval creatures with a craving for heat. The Doctor is accidentally transported "sideways in time" by the partially repaired TARDIS control console into a parallel universe where the drilling project is at a more advanced stage. Thwarted by his friends' ruthless alter egos, he works to save both universes.