A UFO manages to evade interception by Moonbase and lands on Earth. However, waiting SHADO Mobiles are confused when the UFO only touches down for a matter of seconds before taking off again. But the following morning two scientists are reported as not turning up for work in the same area. Colonel Alec Freeman investigates, only to be ambushed by an Alien in the ruins of Mersham Abbey. Colonel Paul Foster, still in the area in a Mobile, searches for Freeman when he doesn't report in and is also wounded by the Alien. Realising that the disappearances are all connected, Straker lays an ambush for the UFO which will have to arrive to collect the abducted men. Unknown to the commander, a Moonferry has sighted the UFO and intercepted it, causing a delay in its arrival. On Earth, the helmetless Alien is weakening, which gives Freeman a chance to escape, just as the UFO arrives. With no chance of capturing it, Skydiver is alerted and Sky 1 is able to destroy it. WIth a dead Alien and a destroyed UFO, the only positive aspect is that Freeman and the two scientists were not taken.
Alec Freeman is enjoying a rest in the countryside when he receives an alert to get to the nearby ETT of A UFO nearby. Finding the UFO, Freeman is taken off guard by an Alien - who reveals himself to be Paul Foster! The commander has had a dummy UFO built, and decided to test it on Freeman - if it will fool him, it might just fool the Aliens in a 'Trojan Horse' style strategy. It is not long before a UFO is sighted, and following Straker's plan it is allowed to reach Earth. Freeman drives Foster in a large truck to the ETT and deploys the dummy UFO, with Foster in a spacesuit pretending to be injured. As SHADO forces close in, the real UFO lands and an Alien goes to help. The trick works and Foster fights the Alien, but he is armed with a pistol and a SHADO marksman has to shoot first. The UFO self-destructs, and SHADO are once again left empty-handed.
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.
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.
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..
Hiding their UFO under bush, the Aliens tap an overhead phone wire and send an emergency signal and location to a nearby hospital. An ambulance is despatched in response, but the two men are ambushed by the Aliens. Minutes later, the ambulance returns to the hospital, and the two men show the Aliens where to find Doctor Issacs. The doctor is stunned, and the two controlled men carry him back to the ambulance. Straker has led a Mobile force to find the UFO, and SHADO Headquarters determine the nearest target is Issacs - a specialist in mechanical hearts - at the nearby clinic. The Aliens are already using the two men to raid the clinic stores, but shoot them when they have what they want. One man lives long enough to give a warning, and Straker is waiting. But the UFO self-destructs, and the Alien-driven ambulance is forced to veer off. With Issacs a hostage, Straker has to give chase but a shot from an Alien gun forces the Mobile off the road. London Spaceport is warned, and the Aliens given access to one of the Moon Ferry rockets. Straker is forced to bluff, and tells the Aliens only enough fuel to get two men into orbit has been given. The Aliens appear to argue - one forcing the other off the rocket at gunpoint - but Straker launches the ferry capsule automatically with Issacs aboard. Their hostage lost, SHADO Mobiles close in, but the Aliens destroy themselves and the launchpad rather than be captured. With Issacs safe, the crew of the spaceport are given the amnesia drug to make them forget.
Among the guests are Straker and Freeman, and they are also on the 300mph maiden journey. But unknown to them, the television news helijet has been hi-jacked by Aliens, and they are monitoring the passengers. Using remote control, the Aliens seal the World President's quarters and one gets aboard, stunning him with a gun. By the time the President recovers and the door is released, the Alien has gone. But unknown to anyone, the President is now receiving mental commands from them. UFO activity has been non-existent for the last two months, and Straker suspects they are building up to something big. He is right, for the World President - a guest of the British Prime Minister - now deems SHADO to be an expensive waste in the light of no recent sightings.
SID warns Moonbase of three approaching UFOs, and the Moonbase Interceptors are launched. But one UFO sacrifices itself and self-destructs, screening the other two and allowing them to reach Earth. Sky One is alerted, and lifts off from the Indian Ocean to track the UFOs as they fly over the mountainous Chinese border. But as Carlin moves to intercept, the Chinese military detect the violation of their airspace, and launch missiles. Sky One defends itself but loses the UFOs, leaving Straker, Freeman and Foster to ponder what the Aliens would want in a near uninhabited area of the world...