Decoded signals from a colossal, fifty-mile-long spaceship indicates a major emergency. Koenig orders a mercy flight to the spaceship, taking with him, Helena, Bergman, Alan Carter, Paul Morrow and a security man. They discover that the ship is commanded by agelessly beautiful Kara and a man named Neman, who, along with twelve other people, are the only true survivors of a planet called Daria that they left 900 years before. But when Koenig discovers that the Darians have been keeping themselves alive by cannibalistically transplanting organs from a degenerate civilisation in another part of the spaceship, he realises that he and his team must must act quickly if they are to avoid meeting the same fate.
Alpha receives an automated distress signal from the spaceship Daria, telling of a catastrophe that has killed thousands and left hundreds sick and dying. It asks for medical and material aid to save the few remaining survivors.
Unable to communicate with the vessel, Koenig, Helena, Victor, Alan, Paul, and Bill Lowery go to investigate. as they fly over the twenty mile long, five mile wide ship, they are unable to locate a point of entry.
Suddenly the Eagles control systems are "smothered" and they are pulled into a docking area within the ship. They try to break free, but cannot. They decide to enter the Daria to look for survivors, and a way to release their Eagle.
Inside they find several long passages, in various states of ruin. They split up to look around; Koenig and Bergman one way, Carter and Morrow another, and Russell and Lowery wait by the Eagle.
While the others are gone, Helena discovers a door to another passage covered by wreckage. Lowery manages to unblock the entrance and they enter to take a look. Inside they hear sounds. On further investigation, they see two frightened little people. The two are unable to speak, but appear to be running from something.
Helena tries to calm the female, but the male runs down another corridor, when Lowery attempts to follow, he is struck from behind as he passes through the doorway.
Meanwhile, John and Victor are met by two spacesuited figures. While trying to figure out if this is some sort of welcome committee, the two figures pull out their weapons and fire! Elsewhere on the ship, Alan and Paul stopped by wreckage blocking the passage that they were searching and return to the Eagle.
Inside they find the small male hiding amongst the seats. They coax him out and try to find out where Helena and Bill went. They convince him to show them where they were taken.
Koenig awakens on a bed in a pristine area of the ship and is greeted by the lovely Kara. He asks why they were fired upon, when they came in response to the Darians distress call. She explains that the signal was triggered when the all but one of the Daria's nuclear reactors exploded almost nine hundred years ago, and that they were unaware strangers were aboard their ship, and that's why they were fired upon. Koenig asks if they have located the rest of their party. She tells him, they have not, but will search for them.
Helena, Lowery, and the mute woman are taken to an alter where they are judged for "purity". The female mute is judged as a mutant and forced into a disintegration chamber. Lowery is examined, and when they find he has one finger that is shorter than it should be, he is judged a mutant and forced into the chamber and disintegrated.
Kara introduces Koenig to Neman, the commander of the Daria. They explain that their ship was essentially an "Ark" transporting the survivers of their dying world to a new planet. They offer the Alphans the chance to join them, in exchange for supplies and assistance. Helena is examined, and is determined to be clear of physical imperfections, and is to be offered to the God Neman.
The "spirits" are summoned to take her to their God, as Alan and Paul are lead to her location by the male mute. The "spirits" arrive and are the same spacesuited figures that stunned Koenig and Bergman. They grab Helena, and Paul and Alan rush from their hiding place to save her. There is a struggle and one of the "spirits" is stunned. The other forces Helena into a passageway behind the portrait of Neman. Paul manages to leap through before the door closes, and follows them. Alan is being held for the murder of the "spirit".
When the stun effect wears off, Alan shows his captors that the "spirit" is, in fact, a man, and offers to lead them to expose their false God. While Koenig and Victor check the compatibilty of humans and Darians, they discover that the Darians do not have any stores of the components necessary to sustain life, and they are using living bodies for food!
They confront Kara, who explains that they must survive to preserve the DNA of the "pure" Darians in order to ensure the survival of their race. Koenig meets up with Paul who is still in pursuit of Helena. He tells Koenig that the Darians have her.
They find Kara and force her at gun-point to show them where the bodies are taken. She takes them and they find Helena unconscious. Kara is able to revive her and runs off. Alan leads the survivors to the undamaged portion of the ship. They make their way to room with the gene bank.
Neman and Kara enter soon after. Hadin is dangerously close to the gene bank and Neman runs towards him. Hadin grabs him and tells him that he is no God, then proceeds to toss him through the gene bank. He grabs Kara, and Koenig yells for them to stop. Telling them that the only way they will survive is by working together.
Kara asks how they will survive. With the gene bank destroyed, along with the million years of civilization it represents, she asks what future does her people have.
Koenig tells her that the survivors are their future, that they must teach them to live and survive in space, and that they will help them. On the ride back to the base, Helena mourns the loss of Bill Lowery.
Kano, finally able to get through, asks what happened. Alan tells him to ask again some time. Alan asks Koenig if Alpha was in the same postition as the Darians, would he choose any differently? Koenig responds by telling him to remind him to tell him some time.
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