A strange "Moonman" steals original moon samples to gain energy and take revenge on earthlings for conquering the earth's satellite. Bruce and Dick have a visit from an old friend who happens to be an astronaut giving conferences. However, the astronaut's strange behavior tickles the mind of Barbara Gordon, and as Batgirl, wants to know a bit more about this.
A fat, unscrupulous criminal mastermind, Chico, steals the main control for Gotham City's water supply, turns the water into chocolate syrup and wants a ransom. Batman and Robin must go through his candy traps to arrest him and his gang of sweet tooth kids.
Mad Professor Bubbles uses an underwater lab and a trained shark to steal ships that contains pieces for a machine known as "Operation Sunray". Batman, Robin, Bat-girl and Bat-Mite goes to this so-called "Bermuda Rectangle" to try to stop him and his henchmen.
Mr. Freeze's henchman, Dr. Frost, has invented a freezing ray. Freeze and Frost plan to use the ray to freeze Gotham City's Harbor, because they wish to steal a nuclear submarine. Batman and Robin locate Freeze's hideout, but Freeze traps both in blocks of ice. When Freeze leaves on his diabolical mission, he decides to take Robin (still frozen in a block of ice) along, just for kicks. Bat-mite locates Freeze's hideout; soon, Batman is fully thawed and on the way back to the waterfront. Batman then attempts to save Robin and capture Mr. Freeze.
Clayface uses a circus acrobat who looks like Robin to kidnap an Middle Eastern oil baron, while himself morphed as Batman. The Dynamic Duo must prove their innocence with the help of Batgirl and Bat-Mite.
The Evil Zarbor, who comes from the same planet as Bat-Mite, wants to be its ruler. He asks the help of the Rogue Gallery of Villains (Joker, Penguin, Catwoman and Clayface) to capture the Dynamic Duo while he steals nuclear power plants to take back to his own world.
Zarbor escapes his cell and goes to Earth to seek revenge on Batman and Robin. As he turns them into brainwashed villains, Bat-Mite and Batgirl think of a plan to turn them back to normal and neutralize Zarbor once and for all.