Julien tries to settle this by fighting with Fred in the reptile house with sticks. Burt could not take it anymore. Maurice goes crazy after eating Julien's lychee nuts, demanding the loyalty of all of the animals in the zoo. This results in Rico having a ticking time bomb inside his stomach with no way to expel it. 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 revealed that Pinky had taken the real fish.
Alice eventually finds Skipper in the penguin habitat and brings him to the zoo veterinarian, who applies a strong muscle-relaxing cream to his broken flipper and bandages it up before caging him for observation. Not long after, Skipper's fear proves true when most zoo animals save the penguins, Marlene, Maurice, and Julien turn the zoo upside down with chaotic, apocalyptic behavior. After X gains the upper hand and lassos them, the penguins try to cause a sewage pipe to spray sewage on X. But the lemurs thought he was a real ice cream truck. After the car is destroyed, the Penguins notice Kowalski's targetting system was placed inside and thus Rico admits that he disobeyed orders when he took the car out at night. Fred goes back home and sees Antonio, a muscular, male otter, walking through the bushes.
But the stroller soon rolls into a demolition site where the baby gets out and has to be chased around to be reacquired by the penguins. However, because of the lack of his true friends Maurice and Mort , Julien starts to go crazy. The penguins find Burt in a building. It is then revealed that Skipper and Rico had taught Randy some of their commando fighting moves. Meanwhile Skipper wanders what made his tail feathers shake in the first place. Skipper distracts Julien while Kowalski, Rico and Private make a laser that shoots lightning pointed to the sky and hooked to the bell on top of the entrance building.
Eventually, the team manages to get the sleeping Leonard back into the zoo just shy of nightfall, and once night comes, Leonard awakens and spots Marlene and fears her in the same manner he had the penguins, which Skipper chalks up to Marlene apparently having a bad reputation herself. The penguins put their plan into action and obtain several crates of fish from the delivery truck, but when they return to the zoo, Julien tells them that he secretly switched the crates of fish with crates of the fish cakes. Private hears their fight and allows Mason to come to the penguin habitat for a visit. Mort is uninjured but the bomb lands in the robotic zookeeper's hands, and explodes, destroying the robot. Concerned and annoyed by this, Skipper and the rest of the penguins go to the chimp habitat, where Phil is apparently throwing a party with the gorillas and Joey. Marlene then gets mad at Julien and walks away with Fred. Soon, the team is greeted by Lulu, Hans, Savio, Clemson, and Rhonda — all but Lulu former enemies — who cheerfully welcome the penguins to Hoboken and tell them about Frances, a new zookeeper who has made their lives enjoyable, including by letting them use massage chairs.
Since Mason does not know how to help, they go to Marlene for advice, but the penguins take over. But Alice then finds a penny and tosses it into the fountain, wishing she knew what the story was with the penguins. Meanwhile, Julien steals the position of director from Mason. They see a picture of the kid grown up. The two chimps finally become friends again.
A mission by the penguins to then recapture Jiggles ultimately fails when Julien and Kowalski wind up being consumed by it, but they are later expelled from it when Julien reaches down Kowalski's throat to retrieve a fish Kowalski had eaten for lunch to provoke the monstrous mass to release them. Kowalski attributes this to the differential between an alligator's and a penguin's. After stating that April fools is not going to suffice due to it now being August, Maurice explains to Julien about how the April Fools' Day concept works each April 1. At first, all the others think he is cute when he says he gets what he wants. However, the sheep, Randy, soon tells the penguins that he was provoked to bite the boy because the boy had, among other things, beaten on him and had pulled out a clump of his wool. 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.
Skipper then sends himself, Rico and Kowalski back to bed believing that they are having hallucinations. While the pipe is initially clogged with the doll that the girl had originally lost, sewage soon comes out and gets all over X. Julien doesn't want to admit it, but does when Private was about to sit on him. Alice allows the doctor to study penguins, but is strangely hit by the penguins' volleyball. King Julien finally lowers his dignity and apologizes, and his groove is then returned. Furious, Marlene makes Rico regurgitate a crowbar so that she can beat up Julien.
Skipper initially fears the nanites will become another of Kowalski's disastrous inventions, but changes his mind after Kowalski demonstrates that the nanites are programmed to not allow any harm to come to a penguin. Julien finally decides to get through the traps and saves the zoo after getting blown out of their plastic volcano. The penguins , , and do not believe this allegation, and instead set out to investigate what really happened, eventually locating Maurice at a New Jersey dump. Tired of having his inventions fail on him, Kowalski decides to artificially increase his own intelligence. Once the crate gets back to the zoo, Marlene and the penguins arrange for Rhonda to be transferred to the Hoboken Aquarium which does not actually exist. The two chimps finally become friends again. The four participate in a full day of fun and spontaneous activities.
They need to work together to escape from Joey, and eventually do. Julien challenges the penguins to a race around the zoo, with the winner taking both cars. The penguins then raid the zoo storage facility, the lemurs following behind, resulting in two bags of popcorn being taken between them. However, upon setting its power to 10 the highest , Julien's thoughts and words become reality and cause chaos in the zoo until it eventually creates a tornado of telekinetic objects. Kowalski then says that he has a theory on where the real fish ended up, and it is revealed that Pinky had taken them. After trying several tactics, his teammates fail to get him to regurgitate again, so they begin their goodbyes.