SHADO engages in its first battle with the enemy. Sky One cripples an alien ship which crash-lands in a lake. Straker's team capture its pilot, a strange blue-skinned humanoid - and the grim secret behind the aliens' are revealed.
After a pilot is killed when Moonbase operatives fail to give him course change information, the personnel are recalled to Earth for an investigation. A UFO crashes in northern Canada and the same personnel are assigned to the operation to find the UFO.
A SHADO technician, being blackmailed for information by an unknown party, is caught by Freeman, but not before the information is passed. The technician divulges to SHADO the information he gave to the blackmailers and, after much work on the encrypted data, they discover it is part of a plan by the aliens to attack the Moonbase undetected.
An XV-104 test plane wanders into a UFO target area and the pilot, Paul Foster, makes sightings of both the UFO and Sky One. Angry and frustrated that no one believes his story, Foster suspects a cover-up and decides to conduct his own investigation into the activities of ex-USAF Colonel Ed Straker.
Foster, with his radio knocked out and his oxygen line cut, is presumed lost during a confrontation with a UFO on the moon's surface. Foster is found by an alien, and they develop a bond when the alien attempts make-shift repairs on Foster's suit.
When an Alien Limpet UFO causes the destruction of Lunar Module 32, Straker demands a clean-up programme by the International Astrophysical Commission (IAC) to remove hazardous space debris from Earth orbit. But Straker finds himself butting heads with the IAC chairman, who wants a complete shut-down of SHADO operations.
Two members of SHADO dining at a restaurant, see a diner who was part of Dalotek, a moon-based, private company which discovered an alien device that disrupted Communications between Moonbase and SHADO on Earth.
"Important? What can be more important than your own son's life?" Straker faces the toughest decision of his career when his son is critically injured in an accident. The drug that can save his life can only be ferried from New York in time aboard a SHADO transporter - the same transporter that is in the prime position to track an Alien defector on the West Coast of Ireland
Foster is abducted from a health spa by aliens and is taken into space, presumably back to the alien homeworld. However, the UFO is damaged and crashes on the moon. While the Moonbase personnel try to free Foster of the alien environmental suit, he wakes up in the steam room back at the health spa.
Freeman takes over temporarily while Straker deals with a woman apparently determined to investigate what SHADO is all about.
In the woods between Clare Cross and Lingbury, an injured alien stumbles into a lonely cottage and is shot down by Liz Newton and her lover Cass Fowler. Liz and Cass are taken to SHADO HQ for questioning, but when Liz's husband arrives at the cottage, Paul Foster realises that the alien's death was no accident.
Foster is suspected of being a security leak but, during the trial, Straker learns that Foster's apartment was bugged.
Straker gets approval from above to build a probe with a camera that will track a UFO back to its home planet.
Straker recalls his marriage, and the stormy days that followed as he worked covertly to get SHADO up and running and recruited personnel.
John Croxley's talent for extra sensory perception is heightened after his wife is killed when a UFO crashes into their house. With his mind under the influence of the Aliens, Croxley learns the secrets of SHADO and lures Straker and Freeman to the remains of his house - to kill them!
When a Lunar Module is attacked by a UFO, Straker makes a split-second decision that endangers the astronauts, but ultimately saves them. Later, he is surprised to find his authority being questioned by his most loyal officer, Colonel Paul Foster, who spearheads a campaign against him. Then an attempt is made on Straker's life...
Suspecting a UFO to be responsible for the sinking of a freighter, Straker, Foster and Nina Barry investigate in Skydiver. Attacked by an undersea UFO, the submarine is downed on a ledge on the sea bed and the crew are trapped. While Straker fights against his claustrophobia, Nina faces a living nightmare.
A UFO hides in a lake on a country estate of a well-known equestrian, who has since disappeared. When SHADO tracks down the UFO and manages to destroy it, it breaks up and leaves a strange item floating in the lake.
The body of an Alien, recovered after a UFO attack on Moonbase, reveals some startling new evidence which overturns all SHADO's previous theories about the Aliens. For Interceptor pilot Jim Regan, the news has tragic consequences as he becomes possessed by the mind of an Alien held in the body of a Siamese cat!
A Naval vessel shoots down a UFO in the Atlantic, but the Admiralty rejects further investigation into the incident. Straker suspects a cover up and wants to know why, so Foster courts Admiral Sheringham's secretary, Sarah Bosanquet. What they discover could mean the end of all life on Earth.
Reported missing and presumed dead after a UFO incident which has left SID disabled, astronaut Craig Collins turns up alive and well. But as an operation to complete repair work on SID is planned, Colonel Lake and Colonel Grey discover that Collins is not the man he used to be.
A UFO imbues three young people with incredible powers. One blows up a radar station. The second steals fingerprints and tries to get aboard a Skydiver sub, blowing it up. The third, a woman, tries to blow up SHADO HQ.
A mysterious dome is found under the sea, inside of which SHADO finds duplicates of their HQ personnel who are using non-alien technology to spoof SHADO's instructions to Moonbase and Skydiver.
While picking up Lt. Lake at the airport, Straker and Lake find that time has been frozen except for them. Sawdust hangs in mid-air, Lt. Ellis is frozen mid-word on a view screen, and one man is taunting them, apparently working for the aliens.
After a UFO inexplicably destroys itself less than two miles from Moonbase, a mysterious crystal rock is recovered, causes the person in its vicinity to hallucinate. The rock is eventually transferred to Straker's office, where he hallucinates that SHADO is simply a set for a TV series, he is an actor named Mr. Burns, Moonbase can be reached by stepping through two doors from the main control room at SHADO HQ, and 'Mr. Straker' is not available.
A woman awakens from a 10-year coma and begins telling the tale about her encounter with aliens while she and her boyfriend were high on drugs.
