As Julien (Danny Jacobs) and Maurice (Kevin Michael Richardson) fight over a camera that had fallen into their habitat, the flash suddenly fires, resulting in Maurice falling out of the enclosure. However, since Julien sees Maurice's photo on the camera's display, he incorrectly assumes that Maurice became trapped inside the camera for failure to obey Julien's orders. The penguins (Tom McGrath, Jeff Bennett, John DiMaggio and James Patrick Stuart) do not believe this allegation, and instead set out to investigate what really happened, eventually locating Maurice at a New Jersey dump. Although he is initially delighted to be away from Julien, after the penguins' antics in trying to get him home, Maurice is relieved to be back in Julien's kingdom.

After being annoyed by the lemurs, the penguins decide to take a vacation to the moon to get away from them. They launch a rocket to reach their desired destination but, unbeknownst to them, wind up on a rooftop across from the zoo instead of on the lunar surface. There, they meet a stray cat who they believe to be a "moon cat" who takes kindly to the foursome with an ulterior motive to eat them, though he later befriends them for real when given a gift of canned fish. After leaving the "moon", however, the penguins realize they had never left Earth. During the time the penguins are on their mission, Julien and the other lemurs deal with booby traps in the penguins' habitat while trying to "borrow" their TV. Rico coughs up a hammer for Skipper who declares Operation Hammerhead to get revenge on the lemurs for their deception.

Marlene (Nicole Sullivan) screams in the night when a strange sound wakes her up. The penguins and lemurs soon arrive at her habitat to investigate the scream, with Julien performing a song and dance routine designed to scare away the ghostly spirits to which he attributes the noise. However, shortly after the penguins' departure Marlene screams again, prompting them to reinvestigate. In the course of the investigation, Skipper and Marlene are knocked into the sewer underneath Marlene's habitat, where they soon uncover the true origin of the noise: an alligator named Roger who had made the noises in reaction to Marlene's loud snoring.

After reportedly finding an egg in her habitat, Marlene brings it to the penguins, hoping the fellow birds would watch over it. Although not initially wanting to take on the mission, Skipper agrees after Julien purports that the egg was the heir to his throne. As the other three penguins begin to place the egg through potentially dangerous training, Private fears for the safety of "Eggy" and cares for it lovingly on his shift until it is stolen by the lemurs. Once recovered, the little hatchling, a duck (Tara Strong), makes his debut and is soon returned to his mother (Tara Strong).

While trying to prove he can have fun on "Fun Day", Skipper causes Julien's crown to fall into the sewer, making Julien scream for hours. After a visit from an angry Maurice, the penguins set out to retrieve the crown. Meanwhile, Marlene tries to keep Julien calm, while he mourns for his cherished, missing crown. When the penguins find the crown, Skipper has to fight a giant rat (Diedrich Bader) for its return. When the crown is returned to Julien, he finds a smudge on it and calls for his spare crown. Furious at all that work wasted when he had a spare crown the whole time, Marlene makes Rico regurgitate a crowbar so that she can beat up Julien.

After seeing the penguins driving about in their car, Julien requests to drive it, but is denied. Still desiring a vehicle, Julien steals Alice's zoo cart and soon challenges the penguins to a race, with the winner taking the loser's car as a prize. The penguins agree, but after subsequently realizing that their car has no chance of victory in its current state, overhaul it to be race-worthy. In the race, the penguins make a comeback after being subjected to a few cheating maneuvers by the lemurs, only to lose the race when a banana peel dropped by Phil causes the penguins' car to spin-out.

The animals get zoo visitors to feed them popcorn until Alice catches a boy giving some to Marlene. Alice yells at the boy and slaps "Do not feed the animals" signs around the zoo. The animals assemble to determine how to get popcorn on their own, but the penguins and lemurs do not want to work together. The penguins and lemurs each get their own bag of popcorn from zoo storage. When they get back to the zoovenir shop, they find kernels instead. Julien believes they are "popcorn eggs" that need to be hatched. The penguins try interrogating a kernel, but Alice finds a trail of them leading to their habitat. Private and Skipper hide the bag in the incinerator, causing a popcorn explosion. They land in Marlene's habitat and she congratulates them on their job well done. Meanwhile Julien thinks he has been rewarded by the salty snack gods.

Marlene is excited about receiving a new roommate, but Skipper feels the new arrival may have ulterior motives. When Marlene's roommate, a female walrus named Rhonda, arrives, she displays rude and obnoxious behaviors toward Marlene, but Marlene tries to remain positive. However, as the abuses continue, Marlene eventually reaches her breaking point and works with the penguins to transfer Rhonda away. When Marlene subsequently learns that Rhonda is headed for a polar bear reserve, she and the penguins work to reacquire her and reroute her transfer to Hoboken. Skipper's paranoia about Rhonda later proves correct when she is revealed to have stolen Kowalski's invention for Skipper's arch-enemy, a dolphin named Dr. Blowhole.

After cleaning their habitat in record time, the penguins head out for snow cones as a reward. They invite Marlene who initially accepts but panics after finding out the snow cone stand is outside the zoo, revealing she was born in captivity. However, Skipper reassures her that she will be safe with the penguins and Marlene agrees to go. Julien also joins the group without an invitation. Once outside the zoo, Marlene is overwhelmed by the outside world and goes wild. She kidnaps Julien and becomes amorous with him. The penguins manage to find them, but Marlene then carries Julien to the top of Cleopatra's Needle, where the penguins fight her using radio controlled planes. The penguins eventually rescue Julien and trap Marlene in a cage before getting their snow cones and returning to the zoo where Marlene returns to normal.

The penguins try to hide their stray cat friend, Max (from "Launchtime"), from an animal control officer dubbed "Officer X". The penguins try to get him to the sewers, but the entire area outside the zoo has been booby trapped by Officer X. The penguins then hide him in Julien's bounce house, but that fails. They then use Max's scent in Joey's habitat so Joey could take out X, but the reverse happens. Phil and Mason suggest that Max pretend to be a "red Rhodesian slasher" an "ultra-rare, incredibly vicious wildcat", which is coming to the zoo. Officer X at first falls for Max's disguise, but Max accidentally blows his cover while dancing in triumph. He is saved from capture by Alice, who puts him in a cage to mate with a female red Rhodesian slasher. After getting beaten up by the female during the courtship ritual, Max begs for help, so the penguins create a diversion for Officer X by disguising Mort as a rabid Chihuahua. Max escapes, but Officer X catches him, but it turns out to be the female slasher Rico had painted to resemble Max. The female slasher beats up X and Mort sets off all of the traps so Max can escape safely.

A female chimpanzee named Lulu is transferred from the Hoboken Zoo while her habitat is being fixed. Phil falls in love with her and asks Mason (in sign language) to help him win her heart. Since Mason does not know how to help, they go to Marlene for advice, but the penguins take over. The penguins have Mason speak to Lulu for Phil. However, this backfires, with Lulu thinking Mason likes her. The penguins then try having Phil save Lulu first from desperadoes and then a falling crate of bananas, but both plans fail. A love potion and roller disco plan also fail. In the end Phil decides to just speak his true feelings to her via sign language, which Lulu understands except for the last part, which Mason then translates for her. Phil and Lulu fall in love and walk away together.

One night, several of the zoo animals' possessions are stolen. When the penguins learn their TV is gone too, they set out to find the thief. The thief is revealed to be a raccoon with a green hat, looking like Robin Hood, named "The Archer". The Archer eludes the penguins, but in the end they apprehend him. They take The Archer back to their base and confront him, but The Archer explains that he is actually a giver for the zooless. The zoo animals each give him something. The next morning, Private decides to give The Archer a gift, his favorite butterscotch lollipop. They head out and meet up with Fred, a clueless squirrel, who Kowalski first met in "Otter Gone Wild", and after a conversation, they figure out that The Archer is actually a con man by the name of Archie. They chase him down again, but Private throws his lollipop and stops Archie's escape. They force The Archer to be a true hero.

Julien comes to the penguins and announces that his ability to dance has disappeared. In a flashback, Julien recalls how it happened: Jealous that the baboons' dance routine was attracting more attention than his own, Julien dropped a crate of skunks into their habitat, and was cursed in retaliation by lead baboon Darla, trapping his "groove" in a jar. Darla states that she will return the groove if Julien apologizes, but Julien refuses. Later, during a chase, the groove-containing jar is shattered and its magic transferred into Skipper, who uses his newly acquired and undesired dance skills against Julien physically to force him into apologizing to Darla.

The episode starts with Alice bringing in a new addition to the zoo. The new animal turns out to be a frog, named Barry. At first, all the others think he is cute when he says he gets what he wants. When he just lays a finger on Rico's foot, he is automatically poisoned and stunned, and the penguins find out that he is a poison dart frog. The penguins try to get rid of Barry, but Kowalski and Skipper soon get poisoned too. Private has an idea: He creates a robot suit, and tells Barry that he could touch him, but Barry cannot touch Private. Private scares him, but they soon end up hugging. Skipper, Kowalski, and Rico wake up recovered from toxins and find the frog in the penguin's HQ playing Checkers with Private (who is still in the robot suit). Skipper then sends himself, Rico and Kowalski back to bed believing that they are having hallucinations.

When Kitka, a female falcon, crashes at the zoo with a broken wing, a smitten Skipper insists that she stay to recuperate. Though she and Skipper soon hit it off, the other penguins fear that Kitka may want to eat some of the zoo animals, though Skipper rejects these charges. When Maurice later reports that Julien was taken by a falcon, all but Skipper lay the blame on Kitka as they set out to rescue him. Skipper's instincts prove correct, however, when it turns out a male falcon had taken Julien and Kitka was trying to save him. Despite this, Skipper breaks-up with Kitka afterward when she regurgitates Fred.

Bent on an agenda to punish the human race, the penguins' mad dolphin nemesis, Dr. Blowhole, kidnaps King Julien in an effort to lure the flightless force into a trap so that he can annihilate the team once and for all. It is then up to the penguins to spring the trap before Blowhole's plan to flood the Earth comes to fruition.