Sky 1 intercepts a UFO over the north Atlantic and shoots it down over the sea. The Alien survives, and is captured in the net of a new hi-tech fishing ship, where he kills the crew. Ordering the skipper to make a bomb, a signal is sent out to lure Skydiver in to a trap. Skydiver is ensnared by the metal fishing net and the Alien throws an explosive on-board. But the Alien has reckoned without the skipper, who harpoons the Alien, allowing Carlin to get the bomb and throw it into the sea before it explodes.
A top secret chemical called 12X, used for in rocket fuel, is being transported to a new international space base in Cornwall. A UFO evades interception and is tracked heading for the area. Destroying the escort, the Aliens hi-jack the tanker and take it to a disused chemical works. It seems a component of the 12X is a condensed green gas which is also what the Aliens use to breath on their journeys, and Straker must prevent them from obtaining it. Using a dummy alien spacesuit, Straker infiltrates the Alien operation and substitutes a green coloured liquid for the fuel. The Aliens depart but realise the deception and return, destroying the tanker before Sky 1 destroys it. The Aliens have been defeated but the space programme has also been put back...
In the Kentucky backwoods, hillbillies Jepson and Tully see a UFO crashland and an injured Alien stagger out. Foster is in America already and teams up with operative John Gillman to search in a Mobile. But when they find Jepson and Tully's shack, Gillman is shot. The Alien has told them he is a top secret test pilot, and the SHADO men are foreign spies. Having successfully captured Foster, the Alien kills Tully but is attacked by a deranged Jepson. The hillbilly locks Foster in and sets fire to the shack. Foster smashes through a window and follows Jepson, who has returned to the UFO. But Foster's approach triggers the self-destruct and Jepson is killed in the explosion.
Straker is on an inspection tour of Moonbase when UFOs are sighted. Captain Sayers leads an Interceptor flight but the UFOs are able to plant some sort of limpet device on SID before being destroyed. This jams all communications with an ear-splitting sound, and Moonbase is effectively blinded. Sayers volunteers to take an Interceptor and try and deactivate the device but the pilot is really a traitor in league with the Aliens. A massive UFO fleet is massed near Mars and is ready to attack. Seemingly successful in dealing with the device, Sayers returns to Moonbase and attempts to start up the system but he is overpowered. Straker suspected something, and Sayers is found to be wearing ear plugs which protected him - had he started up the system again, the jamming signal would have blown all communications. A back-up mission deactivates the device, and the Alien fleet is destroyed.
Against the background of space - a crippled Earth ship. Astronauts Skipper and Alvin work to repair their ship as an alien ship appears, and a helmeted creature tells them their time has expired! And... cut! Director Sol X. Zimenes congratulates his actors on a 'classic scene' but Buzz Peters, playing the alien 'Terror of the Spaceways', is less than enthusiastic and storms off. Meanwhile, forty miles away outside Los Angeles, a SHADO Mobile closes in on a landing UFO. Both craft are destroyed in an exchange of fire - Operative Hanson is killed, and the Alien pilot is thrown clear, to find a car approaching. The driver thinks this strange figure a publicity stunt, but the Alien steals the car to find a place to hide, and a means to contact base. While Paul Foster heads for the last known position of the Mobile, the Alien passes film studios - and sees a massive spaceship! Crashing through the barrier, the Alien silently bluffs his way to the set, as studio police and crew think him part of a science-fiction film. Foster finds the brutally beaten driver, who dies after telling him about the Alien, and starts to search. The Alien has been found by Buzz Peters, and is killed for his troubles. Before the Alien can get away, he is found by Zimenes, who thinks he is the actor in costume, and is led to the 'spaceship'. Foster arrives as the Alien triumphantly boards it, only to find it is a giant prop! As Zimenes' cameras roll, the angry Alien opens fire, and dies when the 'ship' burns to the ground. With no answers to offer, Foster leaves a baffled Zimenes to put out the blaze.
Alec Freeman reports to Straker that recent events have seen UFOs evade SHADO over the Moldavian Alps. Unable to persuade border guards of their mission, Freeman and co-driver Matthews crash through a barrier and enter Moldavia in pursuit of a landing UFO. The delay cause them to lose the UFO, and they are captured by Moldavian military and brought before Karasko. The leader states the Aliens have commited no crimes against his country, unlike Freeman, and the two are released - without their Mobile - back over the border. Straker decides to use his position as 'film producer' to take a holiday in Moldavia scouting for locations. At Dvarksberg, last known position of the UFO, Straker meets a local who tells him the legend of 'evil dwarves who carried off children', and of a new meaning to this. Straker recognises the pattern of abduction and heads off, but he has attracted the attention of the military. In the mountains, Straker watches a helicopter bring Karasko himself to a cave, where an Alien greets him. Straker steals the helicopter, and uses it to stir up the Moldvian military nearby. They follow when he heads into the cave and hides, leading to a confrontation between army and Aliens. Straker shows the men frozen Moldavians, awaiting transport to the Alien planet, and the military turn on Karasko. The base is destroyed, and the Moldavian major decides perhaps it is time for his country to take its place with the other nations of Earth.
A UFO is destroyed near the Moon by Interceptor One, but jettisons small metal canisters which Interceptors Two and Three cannot hit, even with computer-guided missiles. Moonbase warns Earth, but even Sky One cannot destroy them all. Straker decides to deal with them on the ground, so Alec Freeman and new recruit Hoyle are despatched as the nearest operatives. The canisters seem harmless but when Hoyle impulsively approaches one, he is struck down by gas. Masking his face, Freeman pulls him clear, but Hoyle then turns violent. Knocking him out, Freeman realises if any canisters landed in a town, there would be terrible riots. With no time to waste, Straker parachutes from a SHADO jet to join Freeman, and investigate another nearby landing. This is in the private grounds of the Duke of Brandon but inside, Straker and Freeman have to contend with game animals driven wild by the gas. Climbing a tree to avoid angry cattle, they are saved by a recovered Hoyle, who drives the car under the tree. The mention of shotguns by Freeman gives Straker an idea to counter other landings by canisters. Modified missiles which break up into smaller individual shells are used - just like pellets from a shotgun - and for now, SHADO has won again.
Paul Foster is apprehensive about the idea, forced on SHADO by the Pentagon, and sure enough, two days later Space Scout encounters a UFO. Pursuing it into space outside its operational area, the ship is surrounded by UFOs, and the crew quickly overcome. Two Aliens pilot Space Scout back to Moonbase, and are able to gain control by overpowering Paul Foster. When contact with SHADO Headquarters is restored, Foster uses names of operatives as a code to warn Straker Aliens are in control. As a UFO armada orbits Earth, the Alien commander on Moonbase takes Foster to his UFO, but he makes a break for Space Scout. With a UFO in pursuit, Foster pilots the ship back to Earth. Sky One destroys the UFO, and Foster reports to Straker. The UFOs start their attack, but Pentagon forces are waiting and drive off the offensive. The Alien commander tries to destroy Moonbase in retaliation, but is also killed by SHADO operatives..