Season 3 had 1 official 3 parter (The Londoninium episodes described above in previous post). Season 3 almost had an Olga and Egghead three parter. It was written as three episodes but when it was time to film it was divided up in a two parter and a single episode.
Season 2 had 2 three part episodes. The first 3 parter featured Joker and Penguin and the episodes were: "The Zodiac Crimes", "The Joker's Hard Times", and "The Penguin Declines"
The second three parter feautured Penguin and Marsha Queen of Diamonds and the episodes were: "Penguin is a Girl's Best Friend", "Penguin Sets a Trend", and "Penguin's Disastrous End".
The Zodiac Crimes is the best of the three parters. It even features a getaway by the Penguin using a crane. So you could argue that the crane in Batman66 actually references something from the show.
In the "Zodiac Crimes" Penguin taunts the Dynamic Duo and runs outside to a waiting crane truck. He hopes onto the crane and and is driven away. Batman and Robin run onto the crane to catch him but Penguin uses his umbrella to hook onto an overhead wire and escapes while Batman and Robin are still on the truck.
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