The adventures of four penguins—Skipper, Kowalski, Private, and Rico, who perform various commando-like missions to protect their home in the Central Park Zoo. The penguins often have to deal with problems caused, or made worse, by their zoo neighbors, King Julien XIII (a ring-tailed lemur), Maurice (an aye-aye), and Mort (a mouse lemur).
When King Julien is accidentally bounced out of his kingdom, he is mistaken for a cat and adopted by old lady Gladys.
Kowalski uses an invention to switch King Julian's mind with all the penguins in order to win a contest.
Marlene's fur is bleached when Alice over-chlorinates the otter habitat.
Skipper is accidentally doused with a substance called Inflatium, so whenever he is stressed he swells up like a balloon.
After realizing that Maurice's thumbs could prove to be very useful, the penguins recruit him into their team.
The Penguins are faced with a global battle when their specialty food-making machine belches out a toxic cloud that threatens not just the zoo, not just the city, but the earth itself!
The Commissioner's toupee blows off and soon gets stuck on Maurice's head.
After Rico saves Shelly, she falls for him but things turn a little crazy when she kidnaps his doll in a fit of jealousy.
Ma takes up residence in the Penguins Lair. She smothers the penguins with love and they devolve into a bunch of softies, opening the door for Hans to take advantage.
Marlene wants see a concert but every time she leaves the zoo she becomes a monster!
The other penguins agree to take Private to see "Lunacorns on Ice" to cheer him up.
A putter is at the center of controversy when the Amarillo Kid returns to the zoo.
A stray dog refuses to give up Mort after believing he is a squeaky toy, so the penguins set out to rescue him with the help of Max the cat.
Watching too many ninja movies has brainwashed Leonard the koala. During the day, as he sleeps, he terrorizes everyone by sleepfighting.
Skipper agrees gives a day off from training to the first penguin brings him a kipper.
The penguins need Private's hypercute to escape Alice in order to see their favorite action star at the cinema, but Private's molting renders him unable to engage the talent.
Fred seeks financial advice from King Julien when he stumbles upon an oak tree loaded with acorns, but the Red Squirrel has his own plans for the loot.
A special delivery has come from Madagascar. A baby Fossa!
A hen who seems to have psychic abilities moves into the zoo, and a skeptical Kowalski tries to prove she's a fraud.
Private is tasked with babysitting Eggy and his siblings for Momma Duck while the rest of the team is away, and has to protect the ducklings from the combined forces of the hornets and the sewer rats.
Skipper must prove he can still be a leader when his strength starts to decline.
When Private learns that the Peanut Butter Winkies are going out of production, he urges a raid on the factory and Skipper is so impressed he lets him command the mission.
It's a special day when Bada and Bing get a shipment of delicious plantains to eat. Although they jealously guard the African bananas, King Julien's determined to taste them too.
Skipper's having one of those perfect days, and he decides to use the opportunity to settle an old score.
How in the world is Rico supposed to behave well when King Julien has kidnapped his doll, Miss Perky, with the intention of marrying her?
A former news anchor grows suspicious of the penguins when he begins working at the zoo.
Kowalski invents an enemy detector but it doesn't work. Old enemies are now friends and old friends are now enemies.
The annual Zoo Snooze is here! This year the Vesuvius Twins buy up all the tickets. The zoosters plan to exact sweet revenge on the twins.
The Penguins are faced with a World Domination battle when Private accidentally unleashes KuchiKukhan the Destroyer of Worlds. Can they stop him in time to save the World?
The Space Agency sends Private to the moon. The other birds can't monkey around if they hope to get him home again.
Snowmageddon hits and traps Skipper and Marlene in the convenience store, while Kowalski and Private get snowed into a tree.
When a massive sneeze from Rico causes the underground tunnel system beneath the zoo to rupture, Skipper calls in 4 beavers to fix the situation.
Doris the dolphin's quest to rescue her brother Francis from Seaville brings her to the lovestruck Kowalski.
