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.

"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.

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...

"Unfortunately for them, an Alien came through that door instead of her husband." 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!

Reported missing, 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...

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 personnel are assigned to the operation to find the UFO. Gay Ellis is to coordinate the movement of the mobiles trying to approach the UFO.

A flashback episode in which Straker recalls his marriage, followed by stormy days as he must work covertly to get SHADO up and running and recruit personnel. All this leaves his wife angry at his absence, suspicious at the things he might be doing (her father photographs Straker meeting a woman in a parking garage, a woman who will be working at SHADO). In the end, she gives birth to their son.

A UFO hides in a lake on a country estate of a well-known equestrian, and the equestrian himself vanishes. When SHADO tracks down the UFO and manages to destroy it in an exchange of pot-shots, the UFO breaks up and leaves a thing floating in the water. Treated as if it is a bomb, it is brought back to SHADO and examined, with unexpected results.