As the Alphans are planning to explore the planet Ariel, a 'missile' attaches itself to the en route Eagle. Upon returning to Alpha, the 'missile' gives the Alphans a lunar atmosphere. But the joy at the possibility of making a new world out of the Moon is short lived, as the moon does not enter orbit around the planet or its sun, and Alpha faces destruction from the newly acquired lunar air.
Maintenance technician Fred Clifford is possessed by an eerie yellow glow, which ultimately kills him. It transpires that it is coming from a planet called Triton, which captures the Alphans and insists that Helena should become the Eyes of Triton. Before long she is acting just as Fred Clifford did before his death...
Alien gyphs appear on all of Alpha's screens. Koenig sends an Eagle to investigate. The Eagle is lost and the pilot is taken over by a huge, alien 'Space Brain', using him as a channel to make the Alphans do its bidding. Koenig has to destroy it.
Dan Mateo, the Alphans' botanist, believes that he can communicate telepathically with his plants but collapses. He comes to and appears to be fit and well but he is turning into a murderous and disfigured ghost who has been taken over by an alien manifestation.
The Alphans land on the planet Arkadia, where glyphs suggest it is the cradle of civilisation from which life on Earth began. Now it is desolate and Koenig feels it is unsuitable for colonisation. Two renegade crew members have other ideas, however, and take Helena hostage in their demands to settle on Arkadia.
The Alphans find themselves caught up in a long-running war between two rival planets, Betha and Delta. When Betha appears to have been hit its commander Dione seeks sanctuary with the Alphans. Koenig attempts to negotiate a truce but Dione has other ideas...
An Eagle is sent onto the surface of the planet Psychon, which has titanium, needed for repairs to the Alpha Base. It fails to return and is used by Psychon scientist Mentor as a bait with which to entice other members of the Alphan crew onto the planet. Mentor is building a computer but it will be fuelled by the living brains of humans, and he has his eye on those of the Alphan crew. Fortunately his daughter, the shape-shifting Maya, does not share her father's views and is on the side of the Alphans.
With Maya now a crew member the Alphans discover a young couple called Cantor and Zova who have been in suspended animation for some while. They claim that they are exiles from the planet Golos, following an invasion, and ask for the help of Alphan crew members to restore the planet to them. Helena and Tony accompany them to the planet Golos, where it is apparent that they are not the young innocents they appeared to be.
A transmission from Dr. Logan in Texas City leads the Alphans to believe that they can finally land back on Earth, though they have travelled through time and, when they touch down in Texas City, they will be in the twenty-second century. However, due to a hitch, they find themselves in a barren and hostile environment. It is Scotland in the fourteenth century where the Scots are at war with the English invaders.
A sinister woman called Zamara materializes on the base, forcing Helena and Tony to accompany her to the planet of Vega, whose natives are anything but friendly. A servant of the Vegans, known only as Number Eight, informs the two Alphans that he and his race are the natural inhabitants of the planet and that Zamara and her race are androids, who, it turns out, want the Alphans to teach them warfare.
The Alphans encounter an eccentric and intelligent robot who is known as Brian the Brain. Brian's creator Captain Michael and his crew have all died in mysterious circumstances and Brian asks for the help of Koenig and his crew. However, it soon becomes very apparent that Brian is anything but harmless and was in fact responsible for the deaths of Captain Michael and his colleagues. And he is ready to do the same to the Alphans.
The tall and imposing Magus arrives on board the ship. He claims godlike powers, namely that he effected the Creation. But he is now disillusioned with the way that Life has progressed and wishes to start again. He plans to mate Helena and Tony and Maya with Koenig. But of course he is not God but a renegade cosmic sorcerer, and quite illogical at that, who needs to be controlled.
The latest extra-terrestials to be rescued by the Moon Alpha Base crew are Pasc and his young son Etrec. They are from the usually peaceful planet of Archaron and they claim that they are victims of a rebellion, engineered by Pasc's wife Lyra. However, Helena discovers that they have both been infected with a virus which makes them considerably less friendly and more deadly than their initial claim.
Whilst Koenig and Maya are exploring a planet called Luton,which is lush in vegetation, she picks a flower and he helps himself to some fruit. As a result they are put on trial for murder by three talking trees, the Judges of Luton. The trial is by combat and the pair must face three aliens, one with superstrength, one which can render itself invisible and one which can teleport.
The Alpha Moonbase needs a rare ore known as Milgonite, which is detected on an extremely dry planet. Koenig leads a small landing force and discovers a glowing rock formation which comes alive and cuts off the party's links with the base. It is a trap - the planet needs water to survive and has lured the travellers there for the water in their bodies.
The expansive Taybor, an inter-galactic merchant arrives from hyper-space on his ship the 'Emporium'. He is offering to sell things to the Alphans. Koenig realizes that if the Taybor sold them his space-ship, it would enable the Alphans to fly back to Earth, but the price the Taybor is asking for this transaction is Maya.
Whilst he is exploring an asteroid Koenig is taken over by an alien race known as the Kalthon, who replace him with an exact double. In consequence every action ordered by the fake Koenig is solely for the benefit of the Kalthon and to the detriment of the welfare of the Alphans. Helena realizes that something is wrong when 'Koenig' is cold to the touch and needs to convince the other crew members.
The Alphans land on a planet seemingly devoid of any human existence but being run by a group of machines. The machines explain to the visitors that their human overlords are in a state of regeneration but the chief machine, the Guardian,sees the Alphans as posing a threat and it is down to two newly regenerated females known as A and B to decide their fates.
Ship's engineer Tony Osgood believes he can obtain titanium, to make a new heart for his sick wife Michelle, from the catacombs of the moon, using dynamite. The explosion which follows gives him a vision of the future in which the ship is pursued by a fireball and this comes true. Though Helena is making a new heart for Michelle, Osgood becomes impatient and drags his wife back into the catacombs, giving Koenig a double task - to avoid the fireball and save the Osgoods.
Several crew members explore the planet Sunin, including botanist Shermeen Williams, who appears to have visionary gifts. She links up with an alien, called Vindrus, who wants her help in transferring his body and that of his race, into solid matter, giving them proper human form so that they can join the universe as real matter. However, for every one of his race made flesh, an Alphan must lose their matter.
A strange cloud drifts over the base and causes most of the crew to be stricken with illness. A monster, the 'cloud creature' appears out of the cloud and runs amok on the base. A voice from the cloud explains its purpose. The base must give up its life support in order to prevent the cloud from dying. With most of the crew indisposed through illness, it is down to Maya to employ her shape-shifting skills to beat the creature.
Lambda waves permeate Moonbase Alpha, causing instruments to malfunction and people to behave out of character. Crew member Sally dies in mysterious circumstances. Koenig is assailed by guilt-driven visions from his own past. It eventually becomes clear that the Lambda Variant has amplified psychic abilities on the base, in particular for Carolyn Powell, whose lover was previously Sally's boyfriend, and who is beset by jealous rage. Dr. Russell aids Koenig to overcome his own "ghosts", and prevent Carolyn from taking over the Moonbase.