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.

The Doctor, Jamie and Zoe return to Earth and become embroiled in the schemes of Tobias Vaughn. They meet up with an old friend, Colonel (now Brigadier) Lethbridge-Stewart, and some old enemies, the Cybermen.

The Doctor and Jo visit the Master in his high-security prison on an island off the south coast of England. The governor, Colonel Trenchard, says ships have been disappearing mysteriously at sea. The Doctor discovers that Trenchard and the Master are in league to contact the Sea Devils, a race of reptiles in hibernation in a base beneath the sea, who have been awoken by recent work on a nearby sea fort. The Master intends to use his new allies to help him conquer the world!

The TARDIS arrives on the unnamed planet of the Gonds, who are ruled and taught in a form of self-perpetuating slavery by the alien Krotons — crystalline beings whose ship, the Dynatrope, crash-landed there thousands of years earlier after being damaged in a space battle. The Krotons are in suspended animation, in a crystalline slurry form, awaiting a time when they can be reconstituted by absorption of mental energy. Periodically, the two most brilliant Gond students are received into the Dynatrope, nominally to become "companions of the Krotons", but in truth to have their mental energy drained, after which they are killed.

The TARDIS materialises in Earth's future on a space beacon just before it is attacked by pirates. The travellers find themselves trapped in a sealed section of the beacon. It is blown apart and flown to where the pirates will plunder it of the precious mineral argonite. They witness a conflict between the pirates and the Interstellar Space Corps, led by General Hermack and Major Warne. The ISC are convinced that the pirates' mastermind is an innocent yet eccentric space mining pioneer named Milo Clancey, while their true leader is a man named Caven. Caven has a secret base on the planet Ta. He is assisted by Madeleine Issigri, daughter of Clancey's ex-partner Dom, who - unknown to her - is now his captive. When Madeleine discovers Caven's full treachery, she helps to bring him to justice. The time travellers are given a lift back to the TARDIS by Clancey in his rickety old ship, the LIZ 79.