Ohio State astrophysicist Dr. Allen Hynek is recruited by the Air Force into their top-secret program investigating UFOs called Project Blue Book. Partnered with Captain Michael Quinn, they investigate the case of a military pilot who survived a dogfight with an alien craft. Based on the "Gorman Dogfight" case.

Dr. Hynek and Captain Quinn investigate a West Virginia case of a woman and her two children who witnessed a flying saucer crash near their farm and an alien being emerge from the fiery wreck; based on the Flatwoods Monster case.

When the citizens of Lubbock, Texas witness a mysterious V-shaped craft in the night sky, Hynek and Quinn are brought in to investigate the mass sighting. Based on the “Lubbock Lights” case.

Quinn and Hynek are lead into a secret program involving the Operation Paperclip.

Quinn and Hynek follow clues that lead them to a secret group who have witnessed strange lights.

Mysterious green fireballs nearly cause a nuclear disaster during a weapons test, and Hynek and Quinn must investigate how it could have occurred.

After a Scoutmaster vanishes when he and his troop witness a strange craft hovering in the woods, Hynek is sent to investigate for Project Blue Book, while Quinn is pulled into a rogue mission for General Harding.

When a film emerges documenting an Army platoon under UFO attack, the Generals send Hynek and Quinn in to investigate, where they find the soldiers not only suffer from physical effects of war, but psychological ones as well.