After a decade of work, SHADO (the Supreme Headquarter Alien Defense Organization) is finally up and ready to defend the Earth against the recent Alien attacks. Their first task is to block a detected attack on Col. Freeman as he guards the shipment of some valuable electronic equipment to the SHADO headquarters in England.
During an XV-104 test plane flight, the pilot spots a UFO, and also sees SHADO’s Sky One aircraft which is chasing it. Although the test plane pilot, Paul Foster, reports his sightings, he is rebuffed about his claimed sightings. Foster then decides to conduct his own investigation, which leads him to the activities of the ex-USAF Colonel, Ed Straker.
SHADO finally recovers the body of one of the Aliens, after a UFO attack on the Moonbase. The resulting investigation of the alien reveals the reason why the aliens are targeting the Earth. This information leads to strange consequences for one of SHADO’s operatives.
When a UFO is able to get through S.H.A.D.O.'s security, and destroy a Moonbase module, the Chairman of the I.A.C demands the removal of Straker and the complete shutdown of S.H.A.D.O.
Straker must choose between the life of his critically ill son and stopping a sighted UFO, as the S.H.A.D.O. plane taking his son to “time critical” medical help is the only plane in position to be diverted in time to destroy the UFO.
The UFO Aliens enhance a human’s abnormally high E.S.P. abilities in an attempt to learn the secrets of S.H.A.D.O, and to atempt to kill Straker and Freeman.
Straker’s split second, but controversial decision, which leads to saving the lives of several astronauts from a UFO attack, leads to a subordinate questioning Straker's authority.
A UFO attack leaves Straker, Foster and the crew of a Skydiver trapped on a ledge, deep under water, with little hope of rescue.
Straker uncovers a conspiracy of major proportions when the downing of a UFO by the British navy is found to have been covered up.
When an injured and fleeing alien is shot dead by a couple, it soon becomes apparent the alien was not the real target of the shooting.
S.H.A.D.O gets approval to send a probe to survey and observe the location of the UFO alien’s home world. However, the problem is they first need to find one of the UFO’s, in order to follow it back to its home world.
The UFO aliens have found a way to take over the minds of three humans and give them special powers, and use them to destroy several critical S.H.A.D.O. instillations. However, the third and remaining objective is the S.H.A.D.O. Headquarter itself.
A fatal decompression of a Moonbase sphere turns out to have been caused by a lone bullet fired by a UFO alien. However, Foster’s investigation into the matter, soon puts his life in danger.
A UFO is destroyed near a Moonbase, and a diamond-like stone is recovered. However, the stone turns out to be a plant by the aliens with hypnotic properties. Soon the Moonbase appears to be infested with Mexican bandits, and the aliens appeare to be in S.H.A.D.O. headquarters.
Stryker learns that a S.H.A.D.O. technician is passing vital information to the UFO aliens. What the information is becomes the real question. It is soon learned that it is the secret coordinates of Earth’s Moonbase!
When a UFO attack leaves S.I.D. disabled and an astronaut presumed dead, the astronaut turns up alive and well. However, is he really the same person he was before the UFO attack?
Foster investigates blackouts on the Moonbase, and soon begins to see a link to the Dalotek installation team’s installation on the Moon. When a second blackout causes the deaths of two astronauts while in their lunar modular, Foster must find out who is behind these occurrences, fast.
When Straker and Col. Lake arrive at the SHADO headquarters and find all the personnel in a frozen state in time, they realize that this “timelash” has been caused by the UFO Aliens. The pair must race against time to undo the timelash, before the aliens succeed in their planed invasion.
Foster, tired and hung over from the night before, is required to take part in a mandatory fitness test at the S.H.A.D.O. Research Center, during which he passes out while in the sauna. When he awakens, he believes that S.H.A.D.O. headquarters is under attack by the UFO aliens.
When it appears Foster has divulged secret S.H.A.D.O. information to the media, which could lead to a death sentence for him, it is left to Straker and Freeman to find out who has really leaked this secret information.
When a UFO gets through Earth’s defenses, and an astronaut is killed, Striker believes human error is to blame. Is the intimate relationship between two of the S.H.A.D.O.'s members the cause of this problem?
When Lt. Grey’s first child is born, Straker reminisces about the beginnings of S.H.A.D.O., and the disastrous effect his work has had on his own marriage and his kids.
When an international horse show-jumper goes missing, and a lake is found barren of life, and a mutilated animal corpse is found after S.H.A.D.O. tracks a UFO into a heavily wooded area, can S.H.A.D.O. find the alien link to these events?
Straker is able to discern a new deceptive alien attack strategy, after a freighter is sunk by a missile, and underwater cameraman dies, and they see an unusually heavy UFO activity in one area.
As Straker tries to recover the information obtained from a bug left by a reporter, Freeman has to deal with a Russian mobile Moon rig, which has gone out of control, and is headed to collide with Moonbase.
When a woman awakens from a ten year coma, she gives vital information about a close alien encounter she had in an old abandoned farmhouse. Straker must make sense of her memories in order to unearth the terrifying UFO threat that has lain dormant since she lapsed into her coma.