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.