Eagle One launches from the Moon to investigate a planet dead ahead: Terra Nova. They determine that it has everything it needs to support human life. The lead pilot, Parks, checks in to inform them that there is no signs of intelligent life. Suddenly an energy surge passes through the Eagle, knocking out Parks and his co-pilot. The Eagle One comes down and Koenig, Dr. Russell, and Bergman take a medteam out to investigate. The pilots are unconscious but okay, but they make a startling discovery: there is a third passenger aboard the Eagle. Dr. Russell is surprised to discover that the passenger is her husband, Lee Russell, assumed dead five years ago.
As the doctors examine Lee, Dr. Russell explains that her husband and the rest of the Astro Seven mission were lost in orbit around Jupiter and the ship was never recovered. The computers are unable to detect any of Lee's life signs despite the fact that he breathes. The command crew reviews their options and determines that it will take 20 hours to complete Phase Two of Operation Exodus. They have 72 hours until the Moon passes beyond Terra Nova. Despite the narrow window of opportunity, Koenig orders a 10-hour delay in Phase Two so they can determine what Lee's condition is and what impact it has on their operation.
Lee recovers consciousness and tries to communicate with Dr. Russell. Meanwhile, Bergman suggests that since the instruments are designed to only register known human life signs, something on Terra Nova altered Lee's body so that he's no longer human. Dr. Russell revives her husband and he insists on talking to Dr. Russell alone. Once the others leave, Dr. Russell explains that they need to land on Terra Nova before the Moon passes beyond the planet. Lee touches her, shocking her with energy.
Koenig gets word of Dr. Russell's condition and checks in on her. She's recovered consciousness but doesn't remember anything that happened. She's sure that the man in medlab is her husband Lee. However, Bergman runs medical scans on Lee and discovers that on the initial scan, Lee shows normal human heat patterns. So does the third scan. However, the second scan, when Dr. Russell is absent, shows no heat whatsoever, as if Lee were a corpse. Somehow Dr. Russell's presence is stabilizing Lee.
Lee wakes up and demands to see Dr. Russell. When Dr. Mathias refuses to release him, Lee throws him out of the way with superhuman strength. A security team manages to restrain him and take him to Koenig for interrogation. Lee claims that he's there to help them but refuses to answer their questions. He says that Terra Nova possesses a power beyond their comprehension and inhabitants that they can't perceive. He tells the Alphans not to land on the planet or they'll be destroyed and then dies, his message passed on.
Bergman asks for an extra sixty minutes to run skin tests on Lee's corpse and Koenig reluctantly agrees. Dr. Russell, aware of her husband's death, she assures Koenig that she knows that it isn't his fault and that she long ago came to grips with her husband's death. Bergman calls back to inform Koenig that Lee's body is undergoing reversed polarity, transforming into anti-matter. It's not enough for Koenig to delay Phase Two any longer. He takes a survey team of himself, Dr. Russell, Paul, Sandra, and Alan to Terra Nova, putting Bergman in command.
As the Eagle departs, Dr. Matthias prepares to do the autopsy on Lee but the body breaks apart in a burst of energy. Bergman passes the news on to Koenig, who refuses to abort Phase Two exploration. The Eagle lands on Terra Nova and Carter stays with the ship while the others explore. Koenig and Dr. Russell find fresh water and it tests normal. They transmit a signal to Moonbase Alpha confirming that the water and plants are safe to consume.
Koenig continues the survey but Bergman contacts him to warn that Terra Nova's atmosphere is changing, reacting with the plastic on the Moon. Koenig recalls the landing party as the atmosphere continues to alter, on the Moon and on Terra Nova. Paul's laser explodes, killing him. Next, Sandra's eyes are affected and she loses her sight. Alan warns that the seals on the Eagle are deteriorating and the ship blows up with Alan still inside of it. The Moonbase reactors explode, killing all of the Alphans and destroying the Moon.
Storms sweep across Terra Nova, separating Sandra from the others. Koenig gets Dr. Russell into a crevasse but is hit by debris and killed. Once the storm abates, Dr. Russell goes to the commander, who says that they almost made it before dying.
Lee appears to Dr. Russell and explains that he and the other Astro Seven crew were transformed by radiation and scattered across the universe. He was transformed into anti-matter and found himself on Terra Nova. Lee explains that he can no longer exist in the matter universe and the Alphans can't survive on the anti-matter world of Terra Nova. The longer she is there, the less hospitable the planet will become. When Dr. Russell points out she has nowhere to go, Lee tells her to concentrate and see what she wants to see. The planet reverts to its original friendly appearance and the Alphans are restored to life. Dr. Russell explains what happened and Koenig has no choice but to aboard Operation Exodus and return to Moonbase Alpha.
As the Moon travels past Terra Nova, Kano tries to comfort Koenig by informing him that they should encounter over three thousand planets capable of sustaining them. It will only take 2,500 years to get to them all. Meanwhile, Dr. Russell looks back at the planet that is her husband's new home.