The opening of a time capsule buried at the zoo a century ago, forces the penguins, Julien, Maurice, Mort, Marlene and Fred into a search for the legendary cursed treasure of the Golden Squirrel, which they must find and destroy before the rats claim it for themselves, but matters are complicated when the treasure includes a curse that will drive those who seek it to fight each other until one who is "pure of heart" claims the treasure.
Kaboom and Kabust: After Julien interrupts the penguins' mission to destroy classified files with an undisclosed problem, Skipper dispatches Rico to take care of the matter. At the lemur habitat, Julien complains to Rico about a nearby billboard which he finds bothersome, which Rico soon destroys with dynamite. Having been denied the usage of dynamite in the destruction of the files earlier, Rico greatly enjoys his work, even after the other penguins come over to investigate the blast. Julien then desires more things blown up, but when Skipper warns of the ...
When Skipper is knocked on the head, he's unable to lead the penguins on an important mission.Private accidentally drinks Kowalski's truth serum and starts spilling the penguin's secrets to the rest of the zoo.
The penguins have had enough of the crazy lemurs! They hack into the zoo habitat schematic and successfully transfer the lemurs to the zoo. Finally, peace is achieved. When Roger replaces the lemurs they begin to realize the lemurs weren't so bad.The penguins journey to the bottom of the Atlantic for 100 year-old preserved herring. Skipper, Private and Kowalski chow down on the feast before Rico claims his share. Rico learns he's dodged a bullet when the others contract a food born illness.
An accidental zap from the Fresherizer ray turns Skipper into a baby. The gun tumbles into the sewer, and Kowalski, Rico, and Private leave baby Skipper in Julien's care. They are captured by the Rat King, and baby Skipper must escape in order to help them.The zoo animals are in a panic when word reaches them that the boa constrictor has escaped from the Zoo and is heading to them. They do their best to set up a perimeter, but the snake breaks through and captures them all except Julien.
The penguins are inspired after witnessing a good deed executed by a zoo patron. So they set out to perform their own good deeds -- penguin's style. Mort struggles to liberate Cheezy Bitz from a zoo vending machine so Private stops to help. But when Mort's tail gets hooked onto a dispensing coil, he and Private are sucked into the machine. Each attempt to escape drastically fails. Their only hope for freedom is to be rescued.
Kowalski's invention that stops time falls into the worst hands possible. King Julien's. The lemur breaks it trapping the two in a world frozen in time. Instead of being a disaster they realize they can do everything their hearts desire.Agent Buck Rockgut makes a triumphant return. While hunting the Red Squirrel across the globe, bird contacts the penguins with a warning that the squirrel has a brainwashed sleeper agent among them. They battle each other to a standstill to uncover the agent.
The zoosters think Julien has caused Gladys to slip, cutting off treats she brings them. The rush to judgment condemns the lemur to a swat from the Rump Whomper. Skipper insists Julien is innocent.Kowalski's dream of attending the invention expo have to be put on hold when he's laid up with broken legs. Skipper and the gang go in his place to bring him a full report. The bird goes stir crazy locked away in the hospital, however, and hallucinates that a dangerous Space Squid is invading!
Private has an enemy in the form of Dale the snail. It's because Private smashed the little guy, and keeps smashing him accidentally. Even a public apology ends with Dale getting crushed.Julien becomes enamored of a toilet the penguins have built. He wants to use it as his new throne, only the toilet is actually a stink bomb the penguins built to trap Dr. Blowhole. Julien accidently gets trapped, bound tightly to the bomb, so the penguins must try to stop it from detonating.
Private's big heart overcomes his instinct to flee as he helps a stranded young leopard seal get from New York back to her home in Antarctica. The rest of the team (plus stowaway King Julien) follow in their submarine to make sure the young seal and Private make it in one piece. Problem is, they should have been looking out for themselves - they end up on the menu at the leopard seal village!
The penguins notice it's been quiet at night.The rest of the animals have been sneaking out to spend time partying in the park! The plan to sneak out then return by morning to avoid getting caught by Alice is put in jeopardy when they run into a traffic jam in the tunnel.The penguins make a new friend in Dode the dodo bird, who they clone back into existence after a pesky bout of extinction. Having grown up with no natural enemies, Dode has no fear and it leads him to daredevilish behavior.
Kowalski's obsession with Doris the dolphin drives him to invent a love ray. It works like a charm until Alice falls for a trashcan, Julien falls for Mort, and Skipper orders the ray to be put in reverse. Private gets hit by the reverse ray and instantly loathes Kowalski. Told as a courtroom flashback, Kowalski unwisely revives Jiggles in a small, whipped cream-eating version. The little green cubes multiply on impact, however, and are soon threatening to cover the surface of the earth.