When Batman (West) and Robin (Ward) get a tip that Commodore Schmidlapp (the final role of actor Reginald Denny) is in danger aboard his yacht, they launch a rescue mission using the Batcopter. After a tangle with an exploding shark, Batman and Robin head back to Commissioner Gordon's office where, through deduction and wisdom, they figure out that the tip was a set-up by four of the most powerful villains ever (Joker, Penguin, Riddler and Catwoman), who have united to defeat The Dynamic Duo once and for all.

Armed with a dehydrator that can turn humans into dust, a World War II Unterseeboot made to resemble a penguin, and their three pirate henchmen (Bluebeard, Morgan and Quetch), the "fearsome foursome" intends to take over the world, and Batman and Robin must stop them. Catwoman romantically lures Bruce Wayne into a trap, little suspecting that Wayne is Batman's alter-ego, and Penguin even schemes his way into the Batcave, leaving the Duo unable to prevent the kidnapping of the dehydrated United World Security Council.

After giving chase in the Batboat, the Caped Crusader and Boy Wonder use a sonic charge weapon called "Bat-Charges" to disable Penguin's submarine and bring it to the surface, where a grand fistfight ensues. Although Commodore Schmidlapp sneezes on and scatters the powdered members of the dehydrated Council, mixing them together – which would normally spell their doom – Batman constructs an elaborate filter to return each of them to life.

Prior to this process, Robin asks Batman if it might not be in the world's best interests, with continued problems of overt racism, especially in the U.S. during the 1960s, for them to alter the dust samples so that humans can no longer harm one another. In response, Batman says that they cannot do so and can only hope for people, in general, to learn to live together peacefully on their own.

However, in the final scene, Robin's wishes are ironically fulfilled when the Security Council is improperly re-hydrated. While all of the members are alive and well, continuing to squabble among themselves and totally oblivious of their surroundings, each of them now speaks a completely different language than their original native tongue. As the world looks on in disbelief at this development, Batman and Robin quietly climb out of the United World Headquarters to an uncertain future. Batman's final words express his sincere hope that this "mixing of minds" does more good than it does harm.