The Moonbase command centre gets a reading from Eagle One as it departs a planet that lies ahead of them. They get the initial telemetry on the planet, Terra Nova, and it confirms that it has more than enough resources to support human life. The lead pilot, Parks, inform them that the planet is just like Earth but there's no signs of intelligent life. Suddenly the Eagle is enveloped in energy beams and Alpha loses contact with them. Eagle One continues on course and the crew's life signs show normal. As the Eagle comes in, Koenig sounds a yellow alert and Dr. Russell takes a med team out to the landing bay. The Eagle lands and the med team enter to find both pilots unconscious but alive. However, Professor Bergman finds something startling: another unconscious man in the passenger pod. Dr. Russell identifies him as her husband, Lee Russell.
In medlab, Dr. Russell and her team examine the three men and she notes that her husband was presumed dead for five years after the Astro Seven mission was locked in orbit around Jupiter and lost contact with Earth. Lee displays no vital signs on the instruments despite the fact he's clearly alive. The command crew meets and Bergman notes the only information they have on Lee is Dr. Russell's files. They only have 20 hours for Phase Two of Operation Exodus and a total evacuation will take 48 hours. They'll pass out of range of Terra Nova in 72 hours. Koenig orders the delay of Phase Two for 10 hours to determine Lee's status.
In medlab, Lee recovers conscious and seems to recognize Dr. Russell. He doesn't know where he is and tries to tell her why he came there but passes out. The instruments continue to show he has no life signs. Bergman suggests that the instruments are designed to respond to known biological readings, but something on Terra Nova caused him to adapt so that his life signs are no longer entirely human. Koenig orders Dr. Russell to use a stimulant to revive Lee. She reluctantly does so but he refuse to talk to anyone except Dr. Russell. She insists that her husband has to rest but once they leave, Lee asks where they are. She explains that the Moon has left Earth orbit and they need to colonize Terra Nova. Lee reaches out and touches her and energy shoots from his body, knocking her out.
Koenig is preparing the evacuation when he gets word of Dr. Russell's condition. She's recovered consciousness and is now fine. She doesn't remember what happened and says she simply passed out. Koenig doesn't believe it and asks for an explanation. She insists she simply passed out but assures him that she's sure the man is her husband Lee. Meanwhile, Bergman receives some thermal scans of Lee and shows them to Koenig. The first scan proves normal, but a second scan shows no thermal reading whatsoever. A third scan later reads normal. They realize that the normal scans were taken when Dr. Russell was with her husband.
In the medlab, Lee wakes up and calls to Dr. Russell. She gets up and as he gestures, she unconsciously mimics his gestures. Lee gets up and demands to see Dr. Russell. When Dr. Mathias tries to calm him down, Lee tosses him aside and Mathias sounds an emergency alert. A security team manages to restrain him and Koenig has him brought to his office. As they leave, Koenig tells Dr. Russell to stay away from Lee.
In Koenig's office, Lee explains that he's there to help them. He says he doesn't know how he got to Terra Nova or how long he's been there, and insists they're wasting time with their questions. Lee says that the planet is inhabited but not the way that they think and they can't go near the planet. If they do, a power beyond their understanding will destroy them: their "opposite." They refuse to believe him and he realizes they'll go no matter what he says. Lee sits down and then seemingly dies.
Koenig continues to delay Phase Two while Mathias rushes the autopsy. Bergman asks for an hour to run some skin tests on Lee and Koenig grants him the extra sixty minutes. He advises Koenig to tell Dr. Russell that her husband is dead. Koenig tells her and she agrees that it isn't his fault for pursuing the interrogation and that she's okay, having already learned to accept his death the first time.
With 30 minutes left to initiate Phase Two, Bergman tells Koenig that there are indications that Lee's body is undergoing reversed polarity, the first stage in a conversion to anti-matter. Once it's complete, it will cause complete annihilation. Koenig insists it's just a theory and doesn't believe it's worth aborting the exodus. He orders the Phase Two landing party and takes Carter, Paul, Sandra, and Dr. Russell on the initial exploration team. He has Bergman stay there to take command if he doesn't return.
As the Phase Two party leaves, Matthias conducts the autopsy. When he touches Lee's body, it explodes in a burst of energy, knocking him and the assistant out. Bergman reports that Lee's body has disappeared and advises that they abort the mission, but Koenig continues for Terra Nova. The Eagle touches down and Carter stays on the ship while the others spread out to survey the area. Koenig and Dr. Russell find a pond and check the water. It tests as normal and they both drink, and then eat of the plants once they check out safe.
As they continue with the survey, Bergman contacts Koenig and warns him that the atmosphere is changing, causing the plastic to dissolve. Koenig recalls the landing party and they head for the Eagle. As Bergman confirms the atmosphere is affecting the Eagles on the Moon, Carter calls in to report that the Eagle is falling apart. The landing party runs for the ship but Paul's laser explodes, killing him. They quickly get rid of their equipment but Sandra realizes that she's gone blind. Koenig heads for the Eagle but can only watch as the ship explodes with Carter still inside. The situation on the Moon deteriorates further and the landing party looks up as the Moon explodes. Storms sweep the planet, separating Sandra from the others. As they search for their comrade, a landslide sweeps down and Koenig gets Dr. Russell into a cavern for shelter before being hit by the debris. A deathly calm settles across the planet as Dr. Russell confirms that Koenig is dying. He whispers that they almost made it before passing away.
As Dr. Russell lies crying. her husband Lee appears before her. He takes her hands as she begs for help, and then explains that he and the Astro Seven crew was affected by radiation, scattering them into deep space and transforming them. He ended up on Terra Nova where he was transformed into an anti-matter image of himself. He can't survive in Dr. Russell's world and she can't survive in his. Lee warns that the situation on the planet will grow much worse the longer she is present. He embraces her and tells her to see what she wants to see. Dr. Russell concentrates and the planet reverts to its initial friendly appearance. Koenig is restored to life and Dr. Russell explains as best she can. The others have been restored as well and Koenig orders everyone back to Alpha while canceling Operation Exodus.
As the Moon continues along its path, Kano assures Koenig that they will go past over ten million planets and statistically, they should pass three thousand Earth-like planets... in the next 2,500 years. Koenig goes to comfort Dr. Russell as she looks back at the planet where her husband exists.