Secret Squirrel's shorts were a parody of the then-popular spy genre, with most of his shorts' elements satirizing those of the James Bond films.

Secret Squirrel served as a secret agent (his designation was "Agent 000"), taking orders from his superior "Double-Q." Secret was assisted in his adventures by Fez-wearing side-kick Morocco Mole, a mole who in many ways resembled Peter Lorre; Morocco was voiced by Paul Frees. The pair fought crime and evil enemy agents using cunning and a variety of spy gadgets, including a machine gun cane, a collection of guns kept inside Secret's coat, and a variety of devices concealed in his hat (which he almost never removed).

After his original series ran its course, Secret appeared again as part of the cast of the 1970s series Yogi's Gang. Years later, Secret and Morocco were revived in the mid-1990s for the program 2 Stupid Dogs, in segments called Super-Secret Secret Squirrel. These segments were very different, in the case of art work, compared to his original 1960's appearance; all the characters inhabiting the world were now animals. In fact, Double-Q (now just called simply the 'Chief' in these shorts) was now a bull. The new shorts also introduced Penny, a female squirrel assistant to the chief. Plus Morocco, whose skin color was red-brownish, was now gray, his blue shirt was now red, his black nose was now a pink-purplish color, and he now wore sunglasses. In addition, Due to the deaths of Blanc and Frees, Secret was voiced by Jess Harnell , and Morocco was voiced by Jim Cummings.

Since then, Secret and Morocco have made very few appearances, but their shorts air from time to time on Cartoon Network's sister cable television station Boomerang.