As the Moon travels through space, technician Regina Kesslann is the first to notice a sudden disturbance around them. They enter a space warp and everyone is sent flying. Equipment malfunctions as they accelerate through the vacuum of space. Regina goes berserk, trying to find a way out, and Dr. Russell tries to calm her down. The Moon and all of its occupants suddenly split in two. Their duplicates slide away as the second Moon moves away from them.
Everyone passes out from the shock. Upon recovering, Koenig orders a complete systems check. Regina is still unconscious and Dr. Russell is unable to revive her. She warns Koenig that her condition is deteriorating. Meanwhile, the crew locate a solar system ahead.
Regina wakes up in the infirmary and insists that there were two moons. She believes that what she experienced was some kind of dream, as she insists that Koenig and Carter are dead. She asks Dr. Russell if the sun is hot and Dr. Russell notices that she has sunburns on her hand.
Dr. Russell reports to Bergman and Koenig that Regina has sunburn and believes that she's living another life on a planet's surface. Bergman suggests that since they accelerated to near-light speeds, Regina might be living a past or future life. In the command centre, the crew scan the approaching solar system and realize that they've arrived in their own solar system, and are approaching Earth. They'll reenter orbit in 45 hours but are unable to contact anyone. Koenig is skeptical at the possibility that random chance put them precisely back in Earth's orbit, but Bergman suggests that Earth is the place they belong.
Regina comes to accept that she's on the Moon and is happy to learn that Alan is still alive. She insists that Alan is her husband. Dr. Russell reluctantly agrees to let her see Alan.
Alan is eager to launch an Eagle probe and investigate before they arrive in orbit. Koenig insists that they should wait until they're in orbit. Dr. Russell calls Alan to the infirmary where Regina is painting. She runs to embrace the surprised pilot, but then backs away in tears, believing he's dead. Dr. Russell sedates her and explains to Alan that Regina believes she's living in the future. She shows Alan the picture of the planet that Regina believes she lives on.
The crew fails to locate any control signal from Earth. Bergman confirms there have been extensive geological changes and continues to map them out. Koenig finally announces the news to the entire crew. In the infirmary, Regina wakes up and confronts her own image, which morphs into a skull-like visage. In her panic she knocks out Dr. Mathias, takes his comlink and runs out into the hallways. When a security guard approaches her, she knocks him out and takes his weapon.
The Moon achieves Earth orbit and everyone celebrates. Regina arrives on the planet and begs them to help her. Koenig tries to calm her down but she opens fire on a console and then runs to Alan before dying in his arms.
Later, Bergman reports to Koenig that Earth has shifted 5-6 degrees on its axis, resulting in major weather changes. Europe is suffering from a new ice age and much of North America is a vast desert. There's only a small area of life in Santa Maria, CA, that might support life. Dr. Russell gives her report on Regina: she has two brains co-existing simultaneously in her skull. At the same time, the Alphans pick up the presence of another Moon in Earth's orbit. They pick up their own navigational signal from the duplicate Moon. Koenig has Alan prepare an Eagle for liftoff.
Koenig and Alan arrive at the alternate Moon's Moonbase and enter on foot. The station is deserted and Koenig concludes that the crew evacuated to Earth. They also find a wrecked Eagle on the lunar surface. Investigating, they find the corpses of… John Koenig and Alan Carter.
Dr. Russell performs an autopsy on the two bodies and confirms that they've been dead for five years and died on impact when the Eagle crashed. Koenig is ready to begin Operation Exodus but Dr. Russell suggests that he wait, warning that the closer they get to Earth, the more likely that whatever happened to Regina will happen to the other Alphans as well.
In the command centre, Bergman confirms that the duplicate Moon is accelerating and will collide with them in 48 hours. He informs Koenig he'll only have 10 hours to explore so that they have the 24 hours necessary to conduct Operation Exodus. Dr. Russell tells Koenig that only he and Alan should go, since they have no living counterparts. However, Dr. Russell admits that she has no choice but to accompany them to make a medical judgment.
The Eagle lands and Koenig, Alan, and Dr. Russell step onto the planet's surface. Exploring, they find a settlement. Koenig approaches and spots an alternate Professor Bergman charting the two Moons in the sky. The commander approaches Bergman while on the other side of the settlement, Alan and Dr. Russell approach a shelter. Alan finds Dr. Russell and Sandra inside, preparing food. Alan tries to stop her but Dr. Russell insists on seeing her future self. Her future self looks up and sees her past self. Sandra screams and the other older Alphans arrive to investigate.
Future-Bergman explains that they may be on a different Earth, and that the other Alphans have dispersed into smaller settlements throughout the area. Paul and Sandra have had children, who are frightened by Koenig given that he died in their reality. Future Bergman assures Koenig that they will one day be able to bring life back to the dead planet, but it has taken every resource they have. He informs Koenig that his future self made the decision to abandon Alpha and resettle Earth.
Future Paul informs Alan that Regina was affected by some manner of phenomena in the sky and died at the same time that the present Regina did.
Dr. Russell goes to see her future self and warns that her Alpha has no choice but to evacuate to the planet. The future Dr. Russell tells her past self that she married John Koenig and now there's nothing for her and her time there is finished. Dr. Russell insists that they can help each other but the future Dr. Russell insists it's not dying but a return to her self. The future Dr. Russell goes outside and comes face-to-face with Koenig. She gives the past-self of her husband a kiss and then collapses, dead. The future Alphans take her away and then return to tell Koenig, Carter, and Russell that if the rest of Alpha comes down there, it will kill them as well. They refuse to let the present Alphans destroy their new lives. When Alan refuses, Paul prepares to attack him but Bergman intervenes and admits that Paul is right and the present Alphans can't live on the planet. He insists that when the two Moons collide, time will reassert itself and normality will be restored. If Koenig and the others aren't on the Moon when they collide, they'll have nowhere to die. Dr. Russell asks Koenig to take them back and the commander agrees.
The Eagle lands at Alpha and the crew watch as the other Moon approaches them. There's a flash of light and the two Moons merge. The Alphans find themselves adrift in a different part of space and they're left to wonder if their counterparts ever really existed.