Captain Black and Captain Scarlet are sent to mars to investigate a mysterious alien signal coming from there. A misunderstanding occurs and the Mysterons vow revenge. They are killed and both become Mysteron agents. Back on earth Captain Scarlet tries to destroy skybase, but he fails, so Captain Black is revived to do the Mysterons bidding.

The Mysterons resurrect Captain Black, who gains control of a worldwide distribution company and a Russian military leader. With the latter they launch an all-out attack against Skybase whilst with the former they transport enough nuclear material to Siberia to create a bomb large enough to crack the world wide open. Meanwhile Captain Scarlet, who is now back to his old self, must earn Captain Blue's trust as they must work together to stop Captain Black. Meanwhile Black's former lover, Destiny Angel, must come to terms with the fact that the man she once loved is now in league with the enemy.

The Angels shoot down a USAF transport plane that was heading for Skybase, but it releases a swarm of cyberbugs, advanced robots the size of a bug that are capable of eating metal and reproducing with great speed. Once they are aboard Skybase, they set about eating their way towards the atomic reactor core. The headquarters will be destroyed unless Scarlet can find a weakness.

Colonel White's curiosity is piqued by a UFO report from the Scottish Highlands where an elderly lady, Mrs Mackenzie, claims to have seen green lights hovering over the Grampian Nuclear Power Station. Scarlet is dispatched in an Albatross to investigate the plant while Harmony takes a break from the nearby Spectrum Flight Training School to visit Mrs Mackenzie, accompanied by Spectrum Cadet Johnson. Arriving at the power station, Scarlet is assured by the Head of Security that not one of the plant's 400 personnel has seen anything unusual, but at Mrs Mackenzie's cottage, Harmony discovers that neither of her companions are what they appear to be...