Dr J. Allen Hynek (Aidan Gillen), a brilliant yet underappreciated college professor, is recruited by the U.S. Air Force to spearhead a clandestine operation called Project Blue Book. Along with his partner, the debonair Air Force Captain Michael Quinn (Michael Malarkey), he is summoned to investigate UFO sightings around the country and use science to discover what really happened.

However, when some encounters cannot be explained away and cases remain open, Hynek begins to suspect that he has been duped by the government into a larger conspiracy to cover up the truth.