It's 1999 and Moonbase Alpha has been built on the Moon to safeguard the nuclear waste shipped from Earth. On September 13, 1999, disaster strikes and the nuclear waste explodes causing a chain reaction that hurls the Moon out of Earth's orbit and into deep space. The adventures of Space: 1999 begin.
Alpha needs titanium to repair its life support system and traces of it are located on the planet Psychon that is near to the moon. However, Koenig and the others soon learn of a sinister mining operation operating beneath Psychon's surface and what it may spell for the Alphans.
A large group of objects suddenly appear in orbit around the moon and when one is retrieved by an Eagle sent to investigate, it found to contain the cryogenically frozen body of a young man. The man pleads for the Alphans to help revive his frozen colleagues though his pleas may not reveal all of his future plans.
Moonbase Alpha learns that there is technology now on Earth that is capable of sending them home. However, the trip home hits an unexpected bump and Koenig, Carter and Dr. Russell find themselves in a strange place and time as a result.
An alien woman named Zamera suddenly appears on the moon and demands that two Alphans accompany her back to her home planet of Vega. Dr. Russell and Tony go with her to Vega and discover a society with two distinct classes that have different plans for the future in mind.
Koenig leads a team to investigate a ship which resembles one launched from Earth years earlier that has landed on the moon. The ship is found deserted save for a mobile computer named Brian, who soon leads the Alphans into a dangerous situation.
The people of Moonbase Alpha are suprised by the sudden appearance in their midst of a man named Magus, who claims he was responsible for the moon's ceasing to move so he could speak to the Alphans. Magus says he has created a planet that is the equivalent of a second Eden and transports Koenig, Tony, Maya and Dr. Russell there for them to see the world. However, the four quickly learn the real truth behind the sights that they see and the peril they face.
A survey below the moon's surface reveals a stasis chamber that the Alphans were unaware of. The chamber is found to contain two aliens, a man and a boy, in suspended animation. Once revived, the man identifies himself as Petrec and the boy Etrec and says they are emissaries from the planet Archanon. As Etrec is befriended, Helen discovers the two have a shared genetic disorder that may spell doom for everyone at the moonbase.
Koenig, Maya and Tony visit the planet Luton, a pluce lush in plants and vegetation. However, Maya and Koenig quickly find themselves in trouble over their innocent actions of picking flowers and eating a few berries. The two are forced into a dangerous trial by combat by the planet's rulers to prove their innocence with a possible outcome of death.
Alpha' s water system needs a rare mineral named Milgonite and scanners detect quantities of it on a barren planet the moon is passing. When Koenig leads a party to the planet to obtain the mineral, the Alphans discover that the rock structures on the planet are sentient and have a need for water, which they intend to take from the Alphans themselves!
An energetic and flamboyant trader known as the Taybor arrives on the moon to trade with the Alphans. Commander Koenig is interested in a drive the Taybor has that could help his people get back to Earth but is unhappy when he discovers that the Taybor want a high price in trade - Maya!
Koenig journeys alone to an asteroid on a collision course with the moon but returns sounding like a different man. Subsequently, Koenig orders a bizarre plan to be carried out and only Maya and a few others can stop him and find out what is truly going on.
Alpha is bombarded by strong electrical waves that seem to be emanating from a nearby planet. After investigation, Koenig determines that the best course of action is to convince the spherical residents of one of the moons that orbit the planet that Alpha poses no threat to them.
An engineer working below the moon's surface in search of a rare mineral needed for Alpha's life support system and the building of an artificial heart for his wife starts to become unbalanced from the stress and pressure weighing on him. To that end, he undertakes a course of action that endangers many even as Koenig wonders if his rantings might be actually coming true.
Maya contracts a strange illness that causes her to hallucinate and go on a wild rampage through the corridors of Alpha. Meanwhile, Koenig and Tony's investigation of a derelict spacecraft hits an unexpected bump and the two must concoct a desperate plan if they are ever to see Alpha again.
Koenig takes a landing party with him to explore the nearby planet Sunim. Once there, a party member's hallucinations quickly create complications for all of Alpha as they are faced with a decision that could decide the fate of a race in another universe.
An Eagle sent to probe a cloud responsible for a mysterious illness infecting most of Alpha returns with a menacing creature determined to take the life support core of Alpha. Can Tony stop the menace before it's too late?
A strange space cloud appears in the vicinty of Alpha around the same time as a technician dies under mysterious circumstances. Before long, Koenig is locked in a battle of wills with a woman whose latent mental abilities have surfaced presumably due to the cloud's proximity.
A faster-than-light Super Swift ship arrives at Alpha, bringing friends and relatives and raising hopes that they will all be able to go home soon. But Koenig, recuperating from a brain injury, sees only hideous aliens in the visitors.
Koenig desperately tries to convince the others that they're only seeing illusions and that the aliens are actually after energy that they can only get by destroying Alpha.
An Alpha crewman starts believing he's psychic and can sense a habitable planet nearby, leading his team to mutiny and endangering Alpha when Koenig finds that the Moon and the planet are actually on a collision course.
An alien space ship approaches Alpha asking for emergency assistance upon contact. They discover that they are a prison transport ship carrying a prisoner called Dorzak to life in prison on an asteroid. However, Maya knew Dorzak and claims he is a poet and not a mass murderer and releases him.
Koenig explores a planet that was devastated by some sort of weapon that killed all the inhabitants but did not affect the plants or destroy any buildings. He discovers that there is life on one of the moons and when he goes to investigate, he crash lands, and realizes that the moon is a prison and the inmates don't know they have no one to go home to.
The Alphans hopes of resettling on a planet of their own seem to be within reach when a seemingly uninhabited and life sustaining planet is located. But when they learn that the planet is already inhabited by a powerful immortal being, it quickly becomes a fight for survival where only the victor may escape alive.
The Dorcons are a race of conquerors who can live forever by transplantation of a Psychon brain stem. Maya, the last known Psychon, is traced to Moonbase Alpha by the Dorcons, who threaten the Alphans with destruction unless Maya is handed over.