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!

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 is dining in London with his daughter Victoria when he receives a report from Lieutenant Green that a Vampire fighter jet has been stolen from the USAF base at Little Marwood and is targeting the Schleswig-Holstein nuclear plant in Germany. While Spectrum's attention is distracted by this latest threat, Victoria is kidnapped and her abductors threaten to kill her unless the Colonel acquires a Spectrum Rhino to assist them in mounting a bullion robbery. White agrees to the demands while Scarlet and Blue attempt to trace Victoria's whereabouts, but they are unaware that the operation is being controlled by Captain Black who plans to bring about the downfall of the Spectrum organization!