Kowalski's enemy detector malfunctions and causes Skipper to believe all of his friends are enemies, and all of his enemies are friends.
When the Vesuvius Twins buy all the tickets to the annual zoo sleepover, the penguins try to plant a seed of good inside the troublemakers.
Private accidentally frees an ancient spirit from its urn, allowing it to wreak havoc on planet Earth in an attempt to destroy it. But much to the spirit's misfortune, instead of possessing Private, it possesses his Lunacorn doll.
Thanks to am impromptu bouncy game, Julian is launched onto a city bus that drops him off downtown.
He is snatched from the street by Gladys who believes he is a stray cat and taken home to live with her other 'cats'.
Kowalski uses an invention to switch King Julian's mind with Rico in order to win a contest.
Marlene's fur is bleached when Alice over-chlorinates the otter habitat.
Skipper is doused with Inflatium and stress causes him to blow up like a balloon.
After the Zoo Commissioners toupee gets stuck on Maurice, Julian & Mort believe its a monster trying to consume Maurice.
Meanwhile the penguins attempt to track down the missing hair piece.
After Rico saves Shelly, she falls for him but things turn a little crazy when she kidnaps his doll in a fit of jealousy.
The Penguins get a new surrogate mother.
The Penguins must rescue Mort from a stray dog who becomes very fond of him.
During a week of intensive team building the other penguins suggest a break, so Skipper assigns them a task. The one who gave bring him a kipper can have 24 hours off of training.
Private's molting & the zoo's new security system keeps the penguins from seeing the morning movie matinee.
After the penguins disturb Fred's tree during a flight training session, it is discovered Fred is sitting on a huge stockpile of acorns & since in Central Park acorns are considered money, he agrees to let King Julian assist him in spending his new found wealth.
Meanwhile, the Red Squirrel plots to take the acorns for himself.
When a new animal from Madagascar arrives at the zoo, King Julian sees it a cold-blooded killing machine despite the fact it so adorably cute.
After Bada & Bing let the penguins in on the zoo's psychic chicken, Skipper decides she needs to be on their team but Kowalski is the only one that sees the hen's true nature.
Private agrees to take care of the ducklings while the other penguins attend the ultimate monster truck show.
However Private becomes overprotective when all the ducklings want to do is enjoy their day.
Meanwhile, Skipper, Kowalski & Rico have trouble getting in to see the show.
After failing to improve upon his obstacle course time, Skipper instates, P.E.L.T., The Physical Endurance Leadership Test, to ensure he is fit enough to remain commander.
Meanwhile Kowalski steps up as team leader.
The penguins are shocked when they find out the Winky factory is shutting down forever.
Knowing this cannot stand, Skipper puts Private in charge of a raid on the Winky factory in Yonkers to acquire the last Peanut Butter Winkies.
King Julien sneaks into the gorilla habitat when Bada and Bing receive a shipment of plantains.
After a string of good luck, Skipper believes he is having a perfect day so he decides to revisit his grand scheme; Omega Sulu.
When Rico's obsession with Princess Miss Perky puts the team in danger he is put on suspension until he can deem himself worthy by filling up a marble jar.
Meanwhile, King Julian thinks Rico's doll is a real princess and decides the penguins have kidnapped her.
Chuck Charles loses his job as a news anchor and gets a new one at the zoo, but tries to get his old one back by exposing the penguins' operation to the world.
When the penguins learn Phil has been chosen to go into space, they devise an scheme that will send Skipper in Phil's place thus giving new respect to penguin kind.
After a freak blizzard traps Skipper & Marlene in a convenience store with Officer X & Kowalski and Private are stuck with Fred in his tree, it's up to Rico to save them.
Rico gets some teenage beavers to fix a collapsing tunnel, but romance interferes with their work.