At the end of the previous series, Jenny Kelly (Melissa Marshall) was badly injured in the final struggle with Silverthorn (John Howard) for the Time Capsule, and must be taken to the year 3000, to be healed there.
The story picks up a month after Jenny and Alana (Katharine Cullen) arrive back to the year 3000. The scientists soon realise that their time travel experiments have gone wrong and that they have altered the course of history. They must send Jenny and Silverthorn back to their respective times, in order to restore the timeline.
Silverthorn, having faked remorse for his crimes, has surreptitiously stolen instructions for building a time gate. With Silverthorn and Jenny back in their own times, Alana and Lorien (Catherine McClements) return to the year 3000, only to discover that it is a radioactive wasteland: The Great Disaster has destroyed the Southern Hemisphere as well as the Northern Hemisphere. They go back to 2500 and find that that era has not been altered, so they realise that it must be something Silverthorn does in 2500 that changes history and leads to The Great Disaster. In order to restore the timeline, Alana and Lorien must discover the cause of The Great Disaster, and prevent it.
The year 2500 is a polluted, miserable dystopia, where GlobeCorp owns everything, and the majority of people live in relative squalor. Clean water and uncontaminated food are hard to come by, although the elite enjoy life in comfortable skyscrapers, and the top leaders live in a colony on the moon.
With the help of Jenny and Nick, Alana must search for the cause of The Great Disaster, while evading capture by the GlobeCops and new villain Draco (Marshall Napier). They must also find a way to stop Silverthorn’s plan to transport water from 1990 to the year 2500, which he does by using the Year 3000 information he has stolen to construct a time gate.