It's the 1960s. The height of the Cold War. The rural town of Granite Flats, Colorado, suddenly becomes a hotbed for mystery and intrigue.

Almost a year after Hershel Jenkins was released from jail, mystery is still a permanent resident in Granite Flats, Colorado. From small concerns plaguing the citizens of the small town to ongoing FBI investigations, Arthur, Timmy, and Madeline are eager to put their developing detective skills to the test. Their sleuthing goes further than ever before, and they may be biting off more than they can chew. And as it turns out, sleuthing is a family affair. The parents of all three miniature detectives have dipped their toes in the water. Chief Sanders works side by side with the FBI to find a citizen who is disloyal to the country, Beth is embroiled in the center of experimental work at the hospital, and the Doctors Andrews are the masterminds behind the shady experiments. This season, everyone has got a secret and nobody is ready to admit it.