Penguin is the main antagonist in the movie and formed the "Animalitia" who composed of Killer Croc, Man-Bat, Cheetah, and Sliver Back. Penguin ordered his goons to rob several places in the futuristic city of Gotham so he can use his company Bumper Mechanics to generate a force field around the Cobblepot Tower and build a magnetic device so he can make the asteroid crash into Gotham City so he can then take the asteroid since it was composed of gold. Fortunately, Batman was able to have help in stopping the Animalitia by Night Wing, Red Robin, Green Arrow (who was in Gotham City for unknown reasons), and the Flash (Cheetah robbed a lab in Central City). Penguin even built an army of animal themed robots to assist his team in their crimes by forcing the scientist Dr. Kirk Langstorm to do it because secretly transforming him into the super villain Man-Bat.
When Batman was able to foil his plan, Penguin abandoned his team by fleeing on a shuttle set for another location. Fortunately, Green Arrow fired an arrow at the Penguin's escape craft causing him to land in the Arctic region and be confronted by various penguins.
Batman Unlimited: Mech vs MutantsPenguin later appears two films later as the hidden main antagonist in the movie, Batman Unlimited: Mech vs Mutants. In this movie, he was working with Mr. Freeze, and was accompanied by a penguin he named Buzz. After the events of the first film, Penguin was still trapped in the Arctic, stuck with Mr. Freeze who is only obsessed with being in cold climates. At the Arctic, Freeze has finished a machine that can turn anything into a giant monster by experimenting it on an isopod. After witnessing this, Penguin suggested to test it on Gotham's strongest criminals. Freeze reluctantly agreed. They break into Arkham Asylum by using a drilling machine, where they've freed Bane, Killer Croc, Clayface, and Chemo, even though Bane and Killer croc don't like each other. They later retreated to an underwater lair where Mr. Freeze started to experiment on Bane, Clayfaceand Chemo. He used their chemical compound to create a formula that he used on Killer Croc and Chemo that transformed them into giants. He then sends the two to turn Gotham City into an ice age. While watching them freeze the city, Penguin distracted Freeze while his pet bird, Buzz, manage to collect more samples for Bane and Clayface. Later, at the streets of Gotham, Mr. Freeze removed his suit and thanked Penguin for his services. But then, he pointed his freeze ray at him for no longer needing him. Little did he knew that Penguin had plans of his own for the formula. Mr. Freeze was shocked to see Bane and Clayface taking the formula which also made them gigantic. He never planned to use the compound on them because they were too unstable. But Penguin didn't care. As the villains were terrorizing the city, Batman and Green Arrow show up, controlling giant robot versions of themselves. They and their robots engaged into battle with these monstrous villains. At the end, the heroes defeated them.
Later, Penguin and Buzz were driving through the streets of Gotham in Freeze's vehicle, where they noticed the ice was melting. Batman appeared in his giant robot and captured Penguin. It was revealed that Mr. Freeze helped the heroes defeat the villains and accepted surrender. Penguin is taken to Arkham Asylum where he was forced to fix the damages he made there. To make matters worse, he shared a jail cell with Joker who started to beat him up. As for his pet Buzz, he was put in a zoo where he fell in love with a female penguin.
- This is the second movie he teamed up with Killer Croc.
- At the beginning of the movie, Mr. Freeze was the main antagonist for creating the formula that made the criminals Killer Croc and Chemo giant. But later on, Penguin betrayed him by giving Bane and Clayface the formula, making him the Bigger Bad.
- He has a penguin as a sidekick.
- This is the second movie in where he betrayed his colleagues.
- In the movie, it was revealed the Killer Croc and Bane are enemies, ever since Killer Croc sold Bane out.
- The formula had a negative effect on Clayface once he tried it out. This turned his body into lava.
- Only Clayface was the one who escaped. Just how the Joker and the Penguin escaped in the last two films.