An evil sea lion named Goldflipper (voiced by Jim Cummings) creates a giant gold magnet that steals golden teeth, which he calls the "Molar-Acoustic-Synctro-Bicuspid-Dental-Magnetic-Electro-Platt-Conductive-Postiviser". Secret goes undercover as a Squirrely Girly Scout to thwart Goldflipper's evil plan and recover all the stolen teeth.
Secret investigates a mysterious candy disappearance caused by a gingerbread man named Greg (voiced by Charlie Adler), who is using ants to steal all the candy in the world, which he will then use to make a giant candy monster.
A sub-atomic quark known as Quark (voiced by Roger Rose) is destroying important monuments in order to make an amphitheater out of North America. Secret has to shrink down to sub-atomic size in order to stop him.
Queen Bea (voiced by B. J. Ward) and her honey bee minions capture Secret during a Honey Bank robbery so that Queen Bea can force Secret's hand in marriage after trapping Morocco in a honey container. Penny comes to his rescue.
During a race against a race car driving rooster named Hot Rodney (voiced by Jeff Bennett), Secret is waylaid by Hot Rodney's orchestrated kidnapping of Morocco.
Morocco receives a mandatory special assignment to hold a "rare" and "cursed" egg for at least three seconds, but has a hard time doing so.
Expensive paintings are stolen on the night of a museum gala. Secret discovers an art-loving, sophisticated chameleon (voiced by Roddy McDowall) has pilfered all the art for his own personal collection. Secret and Morocco then outsmart him by trapping him in a room full of "modern" art, which Chameleon despises.
In an attempt to cut down his expenses, the Chief replaces Secret with Penny and hires Morocco as his secretary.
Note: Snooper and Blabber make speaking cameo appearances at a crimefighters' pub. In the same scene, Undercover Elephant from CB Bears, Hong Kong Phooey and Mumbly make background appearances, while the portraits of Scooby-Doo, Ricochet Rabbit & Droop-a-Long, Atom Ant, Hong Kong Phooey, Mumbly and Dynomutt, Dog Wonder are seen with Snooper and Blabber's portraits.
In a quiz show hosted by a fox, Secret relates the origin of his partnership with Morocco and an encounter with Morocco's evil twin brother Scirocco (voiced by Jess Harnell).
Note: Yogi Bear and Boo-Boo and the Big Dog and the Little Dog make cameo appearances as the other contestants.
Secret, Morocco and the Chief get their bodies mixed up in a de-scrambler owned by a platypus (Roger Rose) and have a hard time catching him in their altered states.
Secret has to stop an opossum named Doctor O. from blocking out the sun with a satellite, but he has to do it blind and in total darkness. The constant darkness also prevents the Chief from using the rest room.
Secret attempts to stop a crazy giant panda called One Ton (voiced by Yoshio Be) from tearing up Chinatown, but he also has strict orders from the Chief not to harm him, because giant pandas are an endangered species. As a result, Secret has to figure out how to defeat the panda without actually fighting him.
Secret must stop an evil shaman goat (voiced by John Garry), who has made a voodoo doll of the Chief in order to gain control over the agency.