On the moon, technician Regina Kesslann reacts to an otherwise undetectable disturbance, but the rest of the Alphans soon sense something as well. The moon passes through a spatial anomaly and picks up speed. As Regina goes berserk, everyone suddenly seems to suffer from double-vision, seemingly splitting in two. The phenomena persists for a few seconds and then the second images slide away through. The shock proves too much and the Alphans collapse. Upon recovering consciousness, the crew complete a full systems check after determining that they've changed position.
Dr. Russell gets Regina to the medlab but is unable to stabilize her. Regina wakes up and believes that she's dreaming. She says that there were two moons and that Carter and Koenig are dead. She talks about being outside in the bright sunlight and Dr. Russell realizes that Regina's hand is sunburned. She briefs Koenig and Bergman on Regina's apparent delusion that she has another life on a planet. Bergman wonders if their travel at near-light speeds has caused Regina's present self to somehow overlap with her memories of the future, or the past.
The Alphans realize they're approaching a solar system and scan it, only to discover that they are somehow approaching Earth. They're unable to raise anybody via radio and will enter orbit in 45 hours. Koenig speculates that something other than random chance is at work, to so precisely place them back where they started. Bergman insists that it's their destiny to return to their point of origin and Earth is where they belong.
Regina accepts she's on the moon but wants to see Alan Carter. She tells Dr. Russell that Carter is her husband and asks to see him, and the doctor reluctantly agrees. Meanwhile, Carter is discussing the situation with Koenig, suggesting they launch an Eagle in advance of their arrival. Dr. Russell calls him to the medbay where Regina is painting. She runs to greet him but then backs away in horror, overwhelmed by memories of his death. Dr. Russell is forced to sedate her and explains the situation to Carter. They look at Regina's painting, which shows environmental domes on a strangely distorted Earth landscape.
As the moon approaches Earth, Bergman scans the surface and determines that the entire planet has undergone massive geological upheavals. While Koenig notifies the crew of the situation and his plans to initiation Operation Exodus, Regina wakes up in the medlab, suffering from delusions of her mirror image transforming into a skull. She knocks out Dr. Mathias and runs through the hallways, attacking a guard. She takes his gun and runs into the command centre as the moon enters its original orbit. Koenig tries to calm her down but she destroys a command console and runs to Carter, dying in his arms.
Later, Bergman completes his scan and informs Koenig that the Earth below them is radically different. It has shifted on its axis, causing a new Ice Age in Europe and vast deserts across the North American continent. The only place capable of surviving life is a small area in Santa Maria, CA. Dr. Russell gives Koenig and Bergman the autopsy results on Regina: a second brain somehow appeared within her skull.
Another shock is in store for the Alphans: as the moon continues in its restored orbit, they see a second moon orbit around the Earth. They determine that it's emitting a duplicate of their own navigational signal and Carter and Koenig take an Eagle to investigate. They find Moonbase Alpha deserted: everyone there undertook Operation Exodus. They spot a wrecked Eagle on the lunar surface and go to investigate. Inside they finds the corpses of themselves. Koenig and Carter brings the corpses back to base and Dr. Russell confirms that they are who they appear to be, and died in the crash five years ago. Koenig prepares to order Operation Exodus But Dr. Russell says that she's not sure what will happen as they go to the Earth's surface. She suggests it's possible that while Regina may have been more sensitive to the stress of duplication, they all could suffer similar symptoms as they get closer to any counterparts they have on Earth.
Bergman learns of a new factor: the duplicate moon is accelerating and will collide with them in 48 hours. Koenig has only 10 hours to make decision and start Operation Exodus with an acceptable safety margin. Dr. Russell advises him that she'll have to go to make a medical assessment, but only Carter and Koenig should accompany her since they are the only ones who can't have duplicates on the Earth's surface.
The trio land in Santa Maria and find a settlement. Koenig approaches on his own and spots a hooded figure charting the two moons. He approaches and discovers the man is Professor Bergman's alternate. Meanwhile, Dr. Russell and Carter enter the settlement on the other side and investigate a shelter. Carter goes first and sees older versions of Sandra and Dr. Russell inside, preparing a meal. Dr. Russell insists on seeing her alternate self, who looks up. Sandra screams in fear and the other alternate Alphans arrive.
Koenig and the alternate Bergman arrive, and the alternate Bergman explains the situation. The Alphans conducted Operation Exodus as planned, but due to economical reasons have divided up into several smaller settlements. In the last five years, several of the Alphans have had children, including Paul and Sandra, who are now married. On the alternate Koenig's orders, the Alphans stripped everything from the moonbase so they could settle and slowly restore Earth to what it was once.
Meanwhile, the alternate Paul takes Carter to Regina's grave. He informs the pilot that their Regina died after the space phenomena appeared in the sky above them, and Carter realizes that she died at the same time that "their" Regina did.
Dr. Russell talks with her counterpart, warning that the Alphans have no choice but to evacuate before the two moons collide. The alternate Dr. Russell explains that she married John Koenig in her reality but with his death, she has nothing. Her time is finished and it's time that she returns to her self. Before she dies, the alternate Dr. Russell goes to Koenig and gives him one last kiss before dying.
The alternate Alphans tell Koenig, Carter, and Dr. Russell that they can't evacuate, since confrontation with a counterpart causes the death of one or both individuals. Carter insists and the situation turns hostile, but the alternate Bergman intervenes. He insists that the two groups of Alphans can't meet, although such a meeting would be inevitable given the restricted area and limited resources. Koenig warns that they have nowhere else to go but the alternate Bergman believes that when the two moons collide, time will reassert itself and normality will be restored. Although skeptical, Koenig accepts his alternate friend's conclusion. Bergman tells them to go quickly because if they're not on their moon before the collision, they'll be stranded in time.
The three Alphans quickly depart and get back to the moon. As the Alphans watch, the two moons collide in a flash of light. There's a shock wave and the Alphans discover that their moon is intact but they've been sent to a totally different area of space. As they continue on their journey, the Alphans wonder how their counterparts will fare, or if they even existed.