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The penguins find out that the fountain in the zoo is magical and can grant anyone wishes. But soon, all of the zoo animals find out about the magic fountain and become power hungry with wishes.
Kowalski, Private and Rico decide to become superheros after reading a few comic books and their new personas might come in handy when they hear about a theif loose in the zoo.
Skipper and Julien decide to switch places for the day to prove to one another just how difficult their jobs are.
When King Julien is accidentally bounced out of his kingdom, he is mistaken for a cat and adopted by old lady Gladys.
A famous art critic gets a hold of the blueprints to one of Kowalski's inventions and puts it on display at a museum when he believes it to be good art.
Mort is declared the new king of the rats due to a birth mark on his tail. But then the penguins hear that Mort is planning to lead the rats to invade the zoo and must find a way to stop him.
After finding out that the factory that makes winkeys shutting down, the penguins of course freaks out, especially Private, who refuse to let them shut down the factory without a few more boxes of winkeys. Impressed by the passion,
Officer X becomes the substitute worker at the zoo while Alice goes on vacation and he is determened to get revenge on the penguins for all the misery they have caused him.
The penguins seek Maurice's help in missions that require an animal with thumbs. King Julien, initially thrilled to not have Maurice around, soon realizes how incompetent he and Mort are without Maurice.
After the penguins witness a boy returning a dropped dollar to a man and calling it his "good deed for the day," Skipper decides that the team will seek to increase the frequency of their own good deeds.
King Julien wants to keep a diamond necklace he found, but the thieves who stole it desperately want it back.
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.
A maternal possum moves in with the penguins after Hans trashes her own home, but her overprotective nature starts to interfere with their missions.
An extinct dodo is brought back to life, but his reckless behaviour puts him in constant jeopardy.
Kowalski creates a time-stopping stopwatch, which freezes all but those touching the device.
Lemme the robot returns from his Mars mission, but brings back with him an evil space squid which the penguins and lemurs must stop from taking over the planet.
The penguins receive a video message from Buck Rockgut informing them that the Red Squirrel had somehow brainwashed one of them into being a sleeper agent, but he accidentally disconnects himself before revealing who it is.
Private and Mort are trapped inside a vending machine after Private tries to help Mort procure a snack. After determining the two to be missing, the other penguins and Maurice begin to search for them.
Private is tasked with babysitting Eggy and his siblings while the rest of the team goes to a monster truck rally, but then ends up having to protect the ducklings from the combined forces of the hornets and the sewer rats.
Skipper attempts to break his record on the obstacle course, but fails as he comes tenths slower than ever every time, worse than the last. Skipper decides to do P.E.L.T. to prove he is a leader. Meanwhile, Kowalski takes over as "Commander Kowalski" & begins using a binder of missions
Skipper chooses to reward Private for his valient effort on missions by taking him and his fellow Lunacorn fans to see "Lunacorns on Ice" - Bing and Roy!
Mort becomes addicted to a video game that he found in the lost and found box until Kowalski steals the microchip for it so he can use it for his new invention. But then Kowalski feels very guilty for what he did to Mort and he tries to make things right.moreless
When Marlene's fur is accidentally bleached when Alice over-chlorinates her pool, the boys go completely gaga over her believing she's a beautiful Arctic mink named Arlene.
After the other penguins complain about the strenuous tasks they are made to perform as part of Skipper's annual Teambuilding Week, Skipper decides to grant whichever of his teammates brings him a Skipper first one day off from teambuilding exercises. However, things don't go so well when Officer X, now known as Fishmonger X, is employed at the fish market and captures Kowalski, Private, and Rico.moreless
The penguins have to stop an overeager repairman who's about to find their secret headquarters.
Skipper is accidentally doused with a substance called Inflatium, so whenever he is stressed he swells up like a balloon.
Mort gets mistaken for a toy by a dog called Elmer; the penguins uses Max the "moon cat" for a distraction.
The Penguins try to take a relaxing trip to Cape Cod, but a storm ends up taking them to a place that none of them would ever want to be stuck in: Hoboken, New Jersey! If that wasn't bad enough, the Penguins get taken to the Hoboken Zoo were to their horror, nearly every single rude, mean, nasty, or evil animal that the Penguins have ever faced off against are located here! Although the animals have claimed to be reformed, Skipper is certain that there must be something sinister hidden behind and/or beneath the seemingly delightful exterior of the Hoboken Zoo. Is the Hoboken Zoo really more than what it appears to be on the outside, or is it really a nice play to stay? Also, in a B story, when the Penguins are found to be missing, the lemurs decide to help themselves to the TV in the Penguins cave, only to have King Julien frustrated when he is not able to find the remote control that can change the channel.moreless
The penguins' new food-making machine releases toxic substances into the atmosphere, which causes a dangerous increase in climate change.
Against Alice's prohibition, a woman named Gladys sneaks various snacks to the zoo animals, as she had done previously.
While Kowalski tests his new 'Next-o-Skeleton' body armour, Private is shocked and hurt to learn that he has an 'arch-enemy' in the form of Dale, a snail who accuses Private of stepping on him the previous spring (It having taken Dale that long to get back to the zoo).
While counting salt and pepper grains, Rico sneezes and accidentally re-activates 'S.T.A.N.K.', a pre-Private experiment to create the ultimate stink-based weapon- in the form of a toilet- to attack Doctor Blowhole, only for the project to be abandoned when Skipper noted that dolphins don't use toilets.
After learning of Savio's escape from Hoboken on a TV news report, the penguins organize an effort to protect the zoo from the vengeful boa.
After the penguins accidentally destory his habitat, Leonard moves in with Joey, but they have a little trouble getting along.
Kowalski creates a team of robots to help the penguins around their lair, only to end up sealing them in it.
When Kowalski's ray designed to freshen spoiled food accidentally hits Skipper before falling down a storm drain, the leader is turned into a baby penguin, albeit retaining much of Skipper's adult personality.
After the penguins catch the gorillas acting suspiciously at night and then attempting to grab a chicken, Bada and Bing inform them that the chicken possesses psychic abilities that have so far resulted in 122 consecutive accurate sports predictions.
Skipper and Julien are captured by the Vesuvius Twins and brought to their house where they are forced to fight each other.
Marlene arranges a game night in the zoo but Skipper isn't too sure about it, Kowalski, Maurice and Mort go to get some candy, but get caught.
The penguins chase a runaway baby stroller through out the whole city.
Convinced that he is experiencing a perfect day where everything he attempts will automatically work out, Skipper attempts to arrange a plan to break into the Danish Embassy to destroy his file and allow him to return to Denmark.
When Julien learns about April Fools, he decides to pull a few pranks on the animals, knowing that he can get away with it if he says "April Fools."
When Rico accidentally destroys the penguins' car, he rebuilds it himself. Only now the car has a mind of it's own and it tries get revenge on Rico for destroying it.
Skipper finds out that Kowalski did not destroy Jiggles and tries to destroy it himself, but everything starts to go wrong.
The penguins switch King Julien's mind with Rico's in order to win a competition.
Annoyed by the lemurs' music, the penguins arrange to relocate them to the adjacent petting zoo and move Roger to the lemur habitat.
Kowalski can't attend a big inventor's expo because his legs are broken.
Hanz, a puffin and old enemy of Skipper's, comes to the zoo and claims that he has changed and wants to be friends. But has he really changed or is it all a big plan to get revenge on Skipper?
After spying on everyone with the others, Private accidentally drinks Kowalski's Truth drink that makes you spill the truth and now Private starts telling all the animals secrets! Can the penguins fix this before Private spills everyone's secrets?
When the zoo animals find out that Maurice has only 24 hours to live, they try to make his lasts day on earth the best. Meanwhile, the penguins try to find a cure for the disease that Maurice has, but have trouble finding the key ingredient for it.
The penguins sneak out of the zoo at night to party with the other animals in the park, but they have trouble getting home by morning.
King Julien sneaks into the gorilla habitat when Bada and Bing receive a shipment of plantains, which results in him and Marlene being forced to go on the run when they give into temptation and eat all of the plantains.
While Skipper went on his solo mission, Dr. Blowhole wipes Skipper's memories away and Dr. Blowhole uses his memories to locate Kowalski, Private, and Rico.
King Julien steals Kowalski's new invention.
Julien creates a resitance force when he believes that Maurice and the other zoo animals are planning to overthrow him.
After Leonard the koala watches a ninja show, he begins to "sleep fight" the zoo animals like he is a ninja so the penguins must a find a way to cure him to stop "sleep fighting" which does work but things turn for the worse when the rats are out to get him.moreless
Private has been secretly performing works of Shakespeare and when he accidentally blurts some quotes from the plays, Skipper thinks its some kind of enemy code and tries to stop it.
Tired of having his inventions fail on him, Kowalski decides to artificially increase his own intelligence. His experiment works for a while, but when it wears off, Kowalski ends up becoming a simpleton with a lack of brain power. Will the new Kowalski make matters for the rest of the penguins easier to handle, or worse?moreless
Rico must be on his best behavior if he wants to get new accessories for Miss Perky (his beloved doll), but this proves hard to do when the doll itself has been stolen by King Julien.
The penguins try to cure Marlene's feral behavior when she steps outside the zoo so she can attend a concert, but their plan backfires when the split results in an increasingly-fearful version of 'regular' Marlene and her enraged feral self manages to escape while the penguins are at the concert.moreless
The penguins wanted to see a horror movie, but they discovered that Alice had installed shields around the zoo that would not let zoo animals out and in, but humans could. It's not a problem for them but the problem arrived when Private starts to molt so it's gonna mind-switching that doesn't go quite as planned.moreless
Shelly the ostrich falls in love with Rico after he saves her from some drying cement, but first she must get Ms. Perky out of the way.
While building a ship in a bottle, the penguins learn from Phil and Mason that their model is of a Norwegian fishing vessel which sunk 100 years ago in the New York Bay with a catch of brined herring.
The penguins try to use Private's cuteness to their advantage. But Private gets fed up with everyone using him and decides not to use his cuteness anymore, even when he and the other penguins are about to be shipped to another zoo.
When a camera accidentally takes a picture of one of the lemurs at the zoo, King Julien thinks that he's trapped inside of the camera. Using their detective skills, Skipper and the gang search for the lemur before the start of the next zoo tour.
Overnight at the zoo, Marlene wakes up with a scream because she heard some creepy noises underneath her habitat. Skipper and the gang are on the case when they hear this news, and eventually wind up in the sewer to come across the culprit behind the freaky noises.
It's Christmas Eve at the zoo and the penguins, along with all the other animals, are in charge of making the zoo into a huge Christmas party for all the little animal kids. But everything has turned to chaos when the animals can't agree on what the party's theme should be and Julien, who is in charge of getting the Christmas tree, steals the tree from the centre square of the city. Skipper realizes that the only one who can help them is Santa Claus and he and Private go on a frantic search to find him before their party is ruined.moreless
When the Commissioner's toupee blows off and gets stuck on Maurice's head, the baboons mistake him for a male and indulge his every whim.
Marlene becomes good friends with the two new badgers that have arrived at the zoo, but they soon start getting on her nerves. When she finally snaps at them, the badgers become very angry with Marlene and they try to make her pay.
Skipper and the gang all decide to go on a vacation after setting off a burglar alarm, Skipper is banned from Denmark though, so they all end up going to the moon, where they meet an alley cat looking for food, but the penguins think he's a moon cat at first.moreless
When a baby fossa (who came from Madagascar) arrives at the zoo, everyone in the zoo is really enjoying the new arrival except for King Julien. When the baby fossa starts to bite King Julien's booty, he dislikes it very much and tries to avoid and get rid of the baby fossa but it turned that the baby fossa thinks of him as a father which Kowalski stated to him. Things aren't looking so good when King Julien managed to send Savio the rattlesnake back to the zoo and Savio tries to eat the baby fossa.moreless
After a few mishpas, Skipper forbids Kowalski from inventing anything. But Kowalski secretly creates an invisibility ray that goes haywire and starts turing everything invisible. Now Kowalski must find a way to stop the ray without Skipper knowing about it.
Private keeps getting injured to see the new zoo nurse he has a crush on.
After getting a kid's balloon back, Skipper mentions something about The Big One. He explains he has been waiting for it to come for months and he hid some plans in a remote area of the zoo for when the big one comes. But it is revealed that they are building a children's zoo on the spot he hid the plans, so now they try to get the plans before The Big One Comes. But Skipper then starts acting like a news reporter. Can Skipper stop acting like a reporter, and can they get the plans in time before the Big One comes?moreless
Kowalski invents a love ray to make Doris fall in love with him, but the device backfires and people start hating him instead.
The Armadillo Kid returns, this time begging for the penguins help because the gophers will steal his shell.
When a bunch of acorns fall of Fred the squirrel's tree, he becomes the richest animal in the park so King Julien suddenly becomes friends with Fred and throws a party for him but problems comes when the Red Squirrel captures both Fred and King Julien to make them confess about Fred's acorn lottery.moreless
When Uncle Nigel comes to visit the penguins, Nigel reveals to Private that that he is a secret agent on a mission to catch the Red Squirrel.
Private meets a very jittery koala who is deathly afraid of penguins.
Private helps a young leopard seal return to Antarctica, and his pals follow him in a submarine. However, danger looms when they get to their destination.
Seeing that Rico is desperate for the new voice box that comes with his doll, the penguins use the voice box from Private's unicorn doll to cheer him up. But the voice starts to say sweet things which cause Rico to turn into a hippie.