Michelle Generoo, the mission control communication commander for the Space Shuttle program, arranges for a secret meeting with Mulder and Scully. She produces an X-ray of the shuttle's Auxiliary Power Unit valve that she believes was tampered with. A shuttle mission was scrubbed at the last possible second when the valve malfunctioned, narrowly averting disaster. Where the X-ray came from, and how the incredibly strong valve could have been tampered with, remains a mystery, though NASA attributes the malfunction to simple mechanical failure. Fearing NASA might overlook the possibility of sabotage to maintain launch schedule, Generoo decided to step forward on her own.

The agents meet with Lieutenant Colonel Marcus Aurelius Belt, a former astronaut who flew on the Gemini Eight mission and is now the current Space Shuttle Program Director. Belt insists that because of tight security and the sophisticated technology involved, it would be impossible for anyone to sabotage the mission by tampering with the valve.

When the next shuttle achieves orbit around the Earth, a technical problem develops. Generoo, whose husband is one of the astronauts aboard the ship, races back to Mission Control in her car. She loses control of her vehicle when a fog bank forms into a sinister face and rushes toward her windshield.

Mulder and Scully rescue Generoo and return with her to Mission Control. They find technicians attempting to rotate the shuttle before it overheats and burns in orbit. Belt orders telemetry signals to be halted, then instructs the astronauts to fly the ship using the onboard computer. Despite some anxious moments, the astronauts correct the problem and regain contact with Mission Control.

A mysterious force that resembles the famous "Mars Face" emanates from Belt's body and floats into outer space. It engulfs the shuttle, creating an oxygen leak aboard the vessel. Belt orders the shuttle astronauts to don space suits and deploy their payload. Generoo becomes convinced that Belt considers the success of the mission more important than the astronaut's lives.

Belt begins having seizures and Mulder and Scully rush to his aid. Generoo assumes command of the mission and orders the shuttle to return to Earth. Belt, however, insists that the ship will burn up upon reentry unless it changes its trajectory by 35 degrees. Generoo becomes convinced that Belt is telling the truth. She gives the order to change trajectory, saving the shuttle.

Belt suffers another seizure. He jumps from his hospital window, plummeting to his death. Mulder speculates that when Belt orbited the Earth in his Gemini capsule years earlier, he was possessed by an alien spirit, and has been fighting to regain control of his body ever since. The force used Belt to sabotage numerous space missions. Realizing what was happening, Belt struggled to correct the alien's sabotage before it was too late. Mulder concludes that Belt sent the valve X-rays to Generoo hoping to expose the potentially disastrous flaw.