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.

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...

When members of the world Security Council start to commit suicide Colonel White sends Captain Scarlet & Captain Blue to invistigate. Captain Blue checks out one of council members computers and reads an email that hypnotizes him, he uploads the computer to Lieutenant Green. Blue drives of road but Scarlet saves him Blue goes into a coma. Scarlet takes him back to skybase. But the virus has spread to Skybase's computer systems.