Two years have passed since the Nestene creature vanished from UNIT's top secret Warehouse... Suddenly and without warning the Nestene strikes, once again using Autons as its deadly foot soldiers. As mysterious UNIT operative Lockwood struggles to unearth the Nestene plan, he finds himself drawn to remote Sentinel Island. There, the population have been caught up in a bizarre frenzy of religious activity. Lockwood is joined by Natasha Alexander, a new scientific advisor with her own, sinister agenda. To defeat the Nestene menace they must both face the terrifying power of a creature from before the dawn of Mankind...

The Stranger (Colin Baker), still stranded on Earth, has escaped his pursuers and found a safe haven under an assumed name. But his former associates want him back and are not giving up the chase so easily, and his lost past is about to catch up with him...