September 9, 1999. On the dark side of the moon, two technicians, Nordstrom and Steiner enter Nuclear Waste Disposal Area Two. They shut down the laser barrier momentarily and enter via a lunar cart. As they start to run tests, they stay in contact with Professor Victor Bergman and Dr. Helena Russell, who are monitoring their brain activity for any disturbances.
Newly appointed Moonbase Commander, John Koenig, is traveling from Earth to the Moon in an Eagle shuttle. Commissioner Simmonds contacts him to inform him that his first priority is making sure the Meta Probe mission goes as planned. Scientists have confirmed that Meta has an atmosphere and can potentially support life. Simmonds warns Koenig that they can't let the recent discovery of a non-lethal virus among the first team of Moon Probe astronauts detail the project.
At Area Two, Nordstrom and Steiner confirm there's no radiation leakage. As they prepare to leave, Nordstrom's brain activity spikes. He clutches at his head in pain, his eyes glazing over. Bergman and Russell order a security team in while Steiner tries to restrain his co-worker. Nordstrom tosses him aside and then runs into the laser barrier. Repelled, he slams into a rock and cracks open his helmet.
Bergman greets Koenig upon his arrival at Moonbase Alpha and warns that, despite Simmonds' claim, the virus is in fact lethal and has killed several of the afflicted patients, crewmembers at the Moonbase. The base's previous commander, Gorski, arrives to inform Koenig that he'll be there for another few days if Koenig needs help. As he leaves, Koenig observes that Gorski is handling his suspension well.
In Koenig's office, Bergman admits they haven't determined the cause of the virus but have eliminated radiation as the cause. Dr. Russell has additional finding but Gorski refused to let her report them. Bergman suggests Koenig talk to her. The commander goes to Russell's office and she explains that the victims all are suffering brain damage but a virus isn't responsible. She explains that there have been nine deaths so far, and Koenig notes that all of the victims worked in Area Two. However, the two afflicted Meta Probe astronauts have never been near Area Two. Russell confirms that the Meta Probe backup crew is unaffected... so far.
Next, Koenig checks in with Moonbase's head pilot, Alan Carter. Carter is reluctant to commit the backup crew on short notice but finally admits they're ready to go.
Simmonds contacts Koenig, who is less than thrilled that Simmonds downplayed the deaths of base personnel. Simmonds offers to send a medical team but Koenig refuses to let anyone else into the Moonbase until they've confirmed the cause of the illness. He does ask Simmonds to stop the shipment of nuclear waste but the commissioner warns that due to political considerations, he can't stop the deliveries. Koenig is forced to bargain, assuring Simmonds that he'll get the Meta Probe launched on schedule if Simmonds stops the shipments. Simmonds agrees to temporarily delay the shipments, but warns that knowledge of the astronauts' illness can't be made public or the finance committee will cut funding.
Koenig calls for two volunteers to go out to Area Two with him. Bergman and a pilot, Collins, accompany him toward the disposal site. Collins flies over Area One, which is no longer in use and functions as a landmark. Koenig has Collins fly low to get a good look at it. They arrive at Area Two and have two technicians check for radiation leaks while they watch from a control center. Collins goes berserk, insisting that he has to get out. He smashes his helmet repeatedly into the viewpoint, throwing aside the other two men. Koenig finally stuns him and gets out of the room just before the viewport cracks and violently shatters.
Back at the base, Koenig has his staff check the recent flights of the afflicted men. One of the Meta Probe astronauts, Sparkman, dies from the illness. Koenig briefs Carter and the other pilots, telling them that he's canceling all flights, including the Meta Prove launch, until they've identified the cause of the illness.
The crew records show that several of the astronauts lost radio contact as they were passing over Area One. The pilots often use the first disposal site as an aerial landmark and the Meta Probe astronauts flew low over the same area during their training missions. Technician Sandra Benes checks the radiation levels of Area One and confirms that they're normal. However, the temperature starts rising rapidly, burning out the monitor cameras. Koenig flies an Eagle out to investigate. The magnetic fields are superheating, disrupting the Eagle engines in the process. Koenig crashes as Area One burns itself out.
Rescue teams get Koenig back to the base and Russell confirms that he's okay. However, she warns him that he's taking dangerous personal risks and advises him not to endanger himself. Bergman confirms that the supposedly stable radioactive wastes at Area One started giving off magnetic energy. He warns Koenig that the same phenomena could occur at Area Two. They send a remote-controlled Eagle to the second site. The magnetic fields are already on the rise and disrupt the ship's engines, causing it to crash.
Koenig notifies Simmonds of the situation and the commissioner comes to Alpha to handle the situation personally. Bergman warns Simmonds that Area Two has 140 times the amount of waste in Area One, and the explosion will be proportionately larger. He suggests that they start dispersing the waste and Simmonds agrees. However, the Eagles begin to malfunction due to the magnetic fields. With all Eagles tied up in waste removal, Koenig sends Carter into orbit aboard Simmonds's ship to monitor the procedure. Simmonds blindly continues to insist that the removal is going well despite the breakdowns but Koenig warns him that glib press statements won't help.
Despite the evac teams' efforts, Area Two begins to ignite. Koenig aborts the mission as Eagles start to explode from the increasing magnetic energy. The waste detonates in a massive explosion on the dark side of the Moon. Everyone at the base is thrown to the floor by the increasing g-force as the explosion blasts the Moon out of orbit and out through the solar system. A desperate Carter pursues in the Eagle rather than abandon them. Finally the crew recovers sufficiently to confirm that they've survived. The initial thrust dies down and Carter catches up to the Moon.
As the Moonbase crew confirms that the base is primarily intact and damage is minimal, Koenig calls up Emergency Plan Exodus. However, the computer lacks sufficient information to apply the plan. Koenig assesses the risk and informs the base crew that they lack the resources to attempt a return to Earth so they're not going to try.
As the Moon leaves the solar system, the crew watch fading TV broadcasts about the massive destruction on Earth caused by the Moon's departure. Earth isn't even sure if the Moonbase crew survived and is unable to launch a rescue. As they proceed ever onward, they pick up a signal from Meta and Koenig wonders if their future lies there.