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.
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.
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.
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.
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,
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
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.
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.
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
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
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
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
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
Mort gets mistaken for a toy by a dog called Elmer; the penguins uses Max the "moon cat" for a distraction.
The Armadillo Kid returns, this time begging for the penguins help because the gophers will steal his shell.
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!
A maternal possum moves in with the penguins after Hans trashes her own home, but her overprotective nature starts to interfere with their missions.
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
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.
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.
The penguins' new food-making machine releases toxic substances into the atmosphere, which causes a dangerous increase in climate change.
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.
Skipper is accidentally doused with a substance called Inflatium, so whenever he is stressed he swells up like a balloon.
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.
The penguins switch King Julien's mind with Rico's in order to win a competition.
When King Julien is accidentally bounced out of his kingdom, he is mistaken for a cat and adopted by old lady Gladys.