The Joker launches a new crime wave with robberies that appear to make no sense, such as stealing hairpins from rich women and a hole from a golf course. But the Joker knows exactly what he's doing. Batman and Robin are in pursuit and eventually invade the villain's headquarters. The heroes are placed in a chamber and are told if they can float for an hour, they'll go free. The Joker then begins to flood the chamber with poison gas. The Joker says the Dynamic Duo may not be able to swim in the gas "but you can drown in it!"

Commissioner Gordon appears to have been assassinated during the opening of a new bridge. A copy of Hemingway's 'For Whom The Bell Tolls' nearly blows up the Batmobile. Both incidents are clues to the Bookworm's latest scheme. Batman and Robin interrogate The Bookworm's henchwoman Miss Limpet but deduce she is leading them into a trap. And while Batman intends to walk right into it, it is Robin who falls first.

When the lease payment for Gotham City fails to be made on time, possession of the city falls into the hands of Egghead. Chaos ensues as the villain fires Commissioner Gordon and bans the Dynamic Duo from city limits. While the criminal underworld enjoys free reign, Batman and Robin search the city charter's fine print for a solution.

The Penguin appears to have gone straight. (Evidently the citizens of Gotham City have short memories; he tried the same trick in season one.) Not only that, he has emerged as the leading contender for mayor of Gotham City, thanks to a little-known provision of the city charter that permits felons to run for elective office. Mayor Linseed, facing almost certain defeat, convinces Batman to run for mayor. This displeases the Penguin, who doesn't want to leave anything to chance. He lures Batman and Robin into a trap and, by episode's end, things don't look good for the Dynamic Duo.

After escaping the Penguin's death trap, Batman still faces an uphill run to defeat the Penguin in the race for mayor of Gotham City. The Feathered Fiend uses every dirty trick he can think of to ruin Batman's reputation. But the Penguin discovers opinion polls aren't what they are cracked up to be. Still, Batman and Robin will need to subdue the villain before his plot can be put down once and for all.

Mr. Freeze is in town, and has begun a new cold wave of terror. He launches "Operation Hate Batman," framing the Caped Crusader as taking a bribe and dressing his own henchmen as Batman and Robin. As the negative press mounts, Mr. Freeze works on his plan to turn the Dynamic Duo into human Frosty Freezies.

The press continues to attack Batman and Robin, thanks to framing by Mr. Freeze. As public animosity mounts, the Dynamic Duo decide to hang up their capes for the time being. But when Mr. Freeze demands the impossible sum of one billion dollars, or else he will cover all of Gotham City with ice, the Caped Crusaders feel compelled to go back into action to foil the frosty villain.

During a party for Batman's crime-fighting anniversary, the Riddler appears and nabs a golden calf filled with money for charity. His next target is the Gotham City Bank, which he floods for an underwater robbery. Although Batman and Robin try to stop him, the villain makes a clean getaway, leaving only a final riddle that stumps the Caped Crusaders. They discover all too late that his next move is an attempt to destroy them, this time with deadly quicksand disguised as strawberry icing atop a giant cake.

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.

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. The Dynamic Duo are on their way when a bomb planted by one of the Joker's henchmen goes off, leaving them unconscious, and their Batcave cut off from the rest of the world.