Series finale. Minerva has been using her "Deepest Secret Extractor," disguised as a piece of equipment at her mineral spa, to discover where her wealthiest customers hide their valuables. With this info in hand, Minerva has been able to pull off a string of robberies with ease. When Batman and Robin's investigation is cut short by the villainess, butler Alfred goes undercover to help foil her criminal operations.

Dr. Cassandra has a grand scheme against Gotham City with her invisibility pills merely the beginning of her tricks.

The Joker is back in Gotham City, this time with his sights set on worldwide domination. He plants rumors of an invasion from outer space, then sets out to gather the Beryllium metal needed to build an actual flying saucer. Batman picks up on his scheme and sends Alfred to check up on a stash of the metal. But when Alfred is mistaken for a mad scientist by the Joker, he is hauled off to the villain's lair along with Batgirl.

While mining for a rare mineral found only under Wayne Manor, King Tut stumbles upon the Batcave.

After his previous battle with the Terrific Trio, Shame now has Batgirl as a hostage. He agrees to a swap when he realizes that Batman and Robin also have Calamity Jan's mother, Frontier Fanny. Batgirl informs the Dynamic Duo of a plan for a "great train robbery" that she overheard as a hostage. The three work to figure out Shame's plan and race to stop him. But when they realize they are too late, Batman attempts to lure him out of hiding with an offer of man-to-man combat.

Shame escapes from prison, and together with Calamity Jan, goes to work on his newest caper. He leaves a cryptic clue for Batman, Robin, and Batgirl describing the first part of his scheme - the robbery of two opera singers. The Terrific Trio decipher his riddle and attempt to stop him, but when Shame breaks out his "fear gas," the three are left quaking in their shoes.

The Penguin contaminates all the printed money with Lygerian Sleeping Sickness in order to claim them himself but is dangerously frustrated by Bruce Wayne's countermove.

Nora Clavicle, a women's rights activist, uses her influence to have Commissioner Gordon, Chief O'Hara, and the whole police force fired and replaced with women. She cuts ties with Batman and Robin, then launches her plan to blow up Gotham City with explosive-packed mice and collect on the insurance. The Terrific Trio look for a way to neutralize her mechanical hordes before it's too late.

Louie the Lilac is in town, planning to corner the lilac perfume market in Gotham City. His concoction requires the glands of several animals, so he kidnaps Bruce Wayne and Dick Grayson to make the extractions. With "Batman and Robin" unable to respond, Batgirl attempts a rescue, only to be captured herself. The trio rely on their wits (and the latest bat-invention) to attempt an escape.

Following a tip from Batgirl, the Dynamic Trio meet up at the Grimalkin Novelty Company, hideout of the Joker and Catwoman. There, they overhear the arch-criminals' plot and secretly trail them to a stash of hidden gunpowder. A careless mistake spoils the villains' evil plan, however, and they are captured and brought before the Gotham City judge. But when the jury seems less than interested in justice, courtroom mayhem ensues.