The Enterprise arrives in a planetary system to find missing Federation historian John Gill. They are attacked by a nuclear missile from Ekos, even though that planet didn't have the technology capable of producing such missiles the last time a report was made. Kirk and Spock beam down and discover the planet is under a Nazi movement that involves the genocide of the neighboring planet Zeon.

The TARDIS is caught by a mysterious force which causes it to materialise in present-day London. Forty years have passed since their adventure in Tibet, and their old friend Professor Travers has succeeded in reactivating one of the dormant Yeti control spheres - only to summon the Great Intelligence back to Earth. The streets of London are choked with fog, Yeti roam the Underground, and a beleaguered team of soldiers and scientists struggles to find a solution before the city falls completely to the invader. A new commander arrives, Colonel Lethbridge-Stewart - but is he really the new commander of the garrison or is he the Intelligence's new human agent? And if he isn't, then who is? The Doctor must find the traitor before the base is overrun by the Web and London falls...