Archer and his gang have come to Gotham City, winning the public's favor with their Robin Hood style deeds of stealing from the rich to give to the poor. Batman and Robin set out to discover the location of their hideout and stop these villains, only to find themselves caught by a trap in the Archer's lair.

Batman and Robin escape their previous peril and are back in action seeking to foil the Archer and his gang. After pulling off a counterfeit job, the villains head for their boat, planning to take their loot safely to Switzerland. The Dynamic Duo set off in the Bat boat to try to stop their escape.

Catwoman makes her return known with a string of robberies. Hoping to lure her into a trap, Batman plants a news blurb giving the whereabouts of a rare canary, but Catwoman is tipped off and arrives prepared. Batman and Robin follow a lead to Catwoman's hideout, the Pink Sandbox, but soon discover that this villain has been waiting for them.

Catwoman disguises herself as a wealthy recluse - Minerva Matthews - to exchange a quarter million dollars for two Stradivarius violins. Once the instruments are safely in her hands, the villain reveals her true identity and demands the cash back. But Catwoman is surprised to learn that her business partner - Zubin Zucchini - is also not who he appears to be.

The Minstrel, a villain with both musical talent and electronic ingenuity, is wrecking havoc with the Gotham City Exchange in an attempt to blackmail the exchange members. When he soon realizes Batman and Robin are equally skilled with electronics, he deems them a threat to his plan and sets a trap for their demise.

Failing to destroy Batman and Robin, the Minstrel enacts "Plan High C." He shakes the building of the Gotham City Exchange, and promises to send it crumbling down if his demands are not met in one hour. Batman assumes cutting off the building's power will thwart the villain, but when that plan fails, it's up to the Dynamic Duo to track down the Minstrel before it's too late.

King Tut has relapsed into his kingly ways, this time showing a marked interest in scarab beetles and apothecary potions. Robin infiltrates their hideout to discover their true intentions, relaying what he hears to Batman, but their plan is put in jeopardy when Robin's presence is detected.

Using resurrected scarab beetles, King Tut concocts an ancient mind control potion, abu raubu simbu tu. Chief O'Hara is the first under his spell, followed shortly by Commissioner Gordon, and when Batman himself is tricked into taking the drug, Tut's plan to control all of Gotham City by tainting the water supply seems close to succeeding.

Ma Parker and her delinquent children are pulling off a crime wave in Gotham City. Batman and Robin round up the gang one by one, but when the arrests seem all too easy, the Dynamic Duo suspect something else more sinister may be up.

Now in charge of the Gotham State Pen, Ma Parker and her jailhouse full of criminal cohorts use it as their base of operations. No one suspects jailed prisoners of the crimes, but a clue picked up by Batman and Robin may lead them right to Ma's whereabouts.

After a robbery aided by a rigged timepiece, Batman and Robin deduce the Clock King must be in Gotham City. Disguised as a pop art expert, the villain brings his latest masterpiece to the Parkhurst Gallery. But everyone is surprised when the sculpture turns out to be more than just a piece of art, and the Clock King makes off with a valuable time-related painting. Batman and Robin follow a clue to the villain's hideout, unaware that a trap awaits them.

Aunt Harriet purchases a clock as a birthday present for Bruce Wayne, unaware that it is a plant by the Clock King. But when the villain learns that a control switch meant for his final caper has been errantly placed on the timepiece, he breaks into Wayne Manor to retrieve it, nabbing some valuable watches in the meantime. Batman and Robin shortly deduce his master plan and race to stop him.

Egghead steals the Gotham City charter. He finds a loophole that could give him control of Gotham City if descendants of the original founding families (including Bruce Wayne) do not pay nine raccoon pelts to Chief Screaming Chicken on time. Not only is he interested in stopping the payment, but Egghead believes he also has a lead on Batman's true identity.

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.

Chandell, the musical virtuoso, visits Gotham City for a piano concert. But unknown to the public, Chandell is being blackmailed into a life of crime by his twin brother Harry, who retains most of the profits. Chandell intends to buy off Harry forever, and he knows just where to get the funds - from the Wayne family fortune. With Batman and Robin out of town, he suspects the robbery will be a piece of cake. However, Batman has been listening to Chandell's concert remotely, and after detecting an anomalous chord, summons Robin back to Wayne Manor to investigate.

Batman and Robin escape Chandell's trap. Once back in the Batcave, they deduce his plan to get the Wayne family fortune by killing Bruce Wayne and Dick Grayson, then marrying the rightful heir, Aunt Harriet. In order to trap the villain, Bruce and Dick fake their own deaths. However, Harry has also figured out his brother Chandell's scheme, and desiring the Wayne fortune for himself, concocts a plan to masquerade as his twin brother.

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.

The Joker pulls off a string of key-related pranks throughout Gotham City, then with his magic box, proceeds to snatch a priceless jeweled key right under the noses of Batman and Robin. The Dynamic Duo wise up to his ways and thwart him at their next encounter. However, the Joker has more devious plans to do away with them both before his final caper.

After a reworking, the Joker's magic box holds the power to alter time forward and backward. Batman and Robin learn of his plans to pollute the city water supply, and butler Alfred is sent to take over as security guard at the water works. Alfred nabs the box upon the villain's arrival, freezing him and his cronies in time, but unwittingly commits a dangerous error when he removes the box's key.

Marsha, the Queen of Diamonds, is after the giant diamond that powers the Batcomputer. With her love darts, she puts both Commissioner Gordon and Chief O'Hara under her spell (and into her custody). When the Dynamic Duo show up, they too are injected with her love potion, and Batman must agree to marry Marsha if he ever wants his friends to be returned.

Hoping to obtain the Batcave's bat-diamond, Marsha searches for a new potion to use on the Caped Crusaders. Batman and Robin do some searching of their own and arrive at the criminal's hideout. But after Marsha douses them with her concoctions, the villainess seems to have a unique bargaining chip - two tiny caped toads - with which to gain Commissioner Gordon's help in locating the Batcave.

Shame is back, and is using stolen vehicle parts to assemble a truck so fast even the Batmobile won't be able to catch him. Bruce Wayne tricks him into stealing his limo, which he (as Batman) and Robin use to track down his hideout. But the villain gains the upper hand in the ensuing fight, and the Dynamic Duo find themselves staked to the ground in the path of a cattle stampede.