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.

Three weeks after losing contact with Elysium Base on Mars, a team consisting of Captains Scarlet and Blue, Destiny and Harmony Angels, and Doctor Gold are sent to find out what happened to the crew. On arrival, they realise it is a Mysteron trap and that they are under attack from an titanium armour-plated research robot named Remote Acquisition Technology (RAT) which carries lasers and a diamond-tipped saw. Under Mysteron control, the RAT has become the ultimate killing machine.

An unidentified space capsule is tracked from deep space, entering the atmosphere to crash-land in the Arctic. Scarlet and Blue discover that the capsule is from the Endeavor II, a manned mission to Jupiter which disappeared fifteen years ago. Inside, two members of the three-man crew lie dead in their cryogenic tubes, but the third is miraculously still alive and revealed to be Commander Lewis - Lieutenant Green's father! Revived on Skybase and cleared by Dr. Gold's DNA test, Lewis is reunited with his daughter who offers to accompany him to the Space Agency in New Mexico. Then Scarlet learns that Dr. Gold had unwittingly performed the DNA test on himself, and the man being escorted to the Space Agency is a Mysteron replicant...

Destiny and Blue pilot the International Space Agency shuttle Mercury on a mission to deploy a new satellite in Earth orbit which will identify Mysteron energy on Mars and thereby provide early warning of imminent attack. As the shuttle achieves final orbit, Destiny suddenly loses control and the Mercury becomes locked into a new flight path. Then Spectrum receives a ransom demand from an extortionist who threatens to initiate the Mercury's re-entry over North America and crash the shuttle on Washington. With a nuclear power cell on board, the consequences are unthinkable - more so if Captain Black locates the extortionist before Scarlet and obtains the shuttle's access code!

Captain Black reveals that, using Mysteron technology, that he now has control over all the digital systems on Earth and can destroy them at will. The Mysterons then speak through the rogue agent, demanding mankind's surrender in twenty-four hours or else they will trigger a world-wide technological failure that will destroy everyone on the planet. With humanity's surrender as the price, how can Spectrum carry on the fight with weapons that do not work?

In the African desert, Spectrum is assisting Professor Susan Todd of Hydra Laboratories with a revolutionary irrigation scheme, seeding the atmosphere with a hygroscopic compound to generate rain. Scarlet joins Todd for the initial experiment, sharing her excitement as the project proves to a complete success and she is caught in a torrential downpour. Back on Skybase, they celebrate with Colonel White and Hydra director Vandamm but Todd suddenly become paranoid and irrational, pulling a gun on Vandamm and taking him hostage. As the situation spirals out of control, the Colonel begins to suspect that the Mysterons have done something to the rain...

Destiny is selected to help test a new flight guidance system at the Aerospace. Research Unit but en route to Falcon Air Base she is ambushed by Captain Black. Shortly after, Destiny is caught on security cameras breaking into an office at the International Defense Force Headquarters and stealing top secret missile launch codes, badly injuring a security guard as she makes her escape. Scarlet is devastated to learn that Destiny appears to have been replaced by a Mysteron replicant and sets out to locate and eliminate the imposter, but the real Destiny is being held prisoner in a clinic where German scientist Janus has developed a device which transforms any face into a perfect copy of another!

Investigating reports of a Mysteron cell operating in Phoenix, Arizona, Scarlet trails a pair of Mysteron agents to a remote desert diner. There he overhears the agents bribing Spectrum flight-engineer Xander Story to smuggle a bomb aboard Skybase, but when he attempts to apprehend them, Scarlet is shot down. Then the Mysterons drive a petro-chemical truck into the diner and Scarlet is incinerated in the explosion. Blue finds Scarlet's body and returns it to Skybase, but Scarlet's injuries are too severe even for the retrometabolisation process and he is pronounced dead. However, Scarlet recovers consciousness to find himself apparently alive and well - until he realises that he has become intangible and none of his colleagues can see or hear him.

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...

Scarlet and Destiny are undergoing interrogation resistance exercises at the Spectrum Training Base in Scotland when the base commander, Astrid Winters, is killed in a car crash engineered by the Mysterons. Resurrected as a Mysteron replicant, Winters returns to the base with the stunning revelation that she represents a faction of the Mysteron Consciousness which does not believe in the war of nerves. Offering to detail how Spectrum can defeat the Mysterons, Winters insists that she can only deliver the information to Colonel White in person, but as proof of good faith she exposes the Mysterons' plans to wipe out Earth's scientific elite in a single strike on the World Science Congress!