Black and Scarlet through a strange set of circumstances find themselves trapped under Arctic Ice. They realize they need to co-operate with the other to get themselves out of the situation.
Black returns to earth, apparently free of the Mysteron's control, and urges Scarlet to return to Mars with him to end the war he began months earlier.
Scarlet and Blue track a stolen Russian tank into the Alaskan wilderness. There they find a whole town overtaken by the Mysterons. Their mission this time is to unleash one of the greatest terrors in the galaxy on the human population of Earth.
A Mysteron spacecraft enters Earth atmosphere and is engaged by the Angel fighter craft. The Mysteron craft avoids destruction and goes on to land in northern Australia. Scarlet and Blue go to investigate.
Scarlet awakens after being killed during a mission to discover he is a ghost. He is aware of a bomb planted on Skybase but must find a way to interact with the crew and warn them of the situation.
A motorcycle gang member steals Captain Occa's Raid Bike, but finds out that he's an alien fighter and he assists Spectrum in finding a Mysteron agent that is carrying something that can kill thousands of people in seconds.
The Mysterons attempt the takeover of a new advance warship the 'Proteus' Their attempt is only partially successful and a running battle evolves between the ships automatic systems and Spectrum agents trapped on board.
Everyone on Skybase apart from Captain Scarlet and Destiny Angel are infected by a deadly virus uploaded on the Skybase computer. Can they erase the virus before they too become infected?
Spectrum becomes aware of a Mysteron plan to penetrate the defenses of a nuclear power plant in Scotland. Spectrum launch every available asset to stop them but discover the Mysterons intend to use Spectrum's own technology to defeat them.
The designer of the devastating Thunder Pulse compression bomb is presumed killed and replaced by the Mysterons. Spectrum turn to his twin brother who is a convicted criminal in the hope he can make some sort of mental link and stop whatever plan the Mysterons are trying to execute.