NOTE: This spoiler was submitted by Jeremy

Ten years ago in Antarctica, a documentary filmmaker (Werner Herzog) is scoping out a colony of penguins. A little egg rolls past them, getting the attention of three rebellious penguins - the brainy Kowalski (Chris Miller), loose cannon Rico (Conrad Vernon), and the leader Skipper (Tom McGrath). They question why the other penguins are letting the egg roll away, to which the older penguins respond that it's just nature. Skipper proudly rejects nature and chases after the egg. The egg rolls over a cliff, with Skipper nearly following, until Rico and Kowalski form a penguin ladder to save him. The filmmaker continues documenting the penguins and has the boom mic operator shove them over the cliff. They and the egg land on an old ship. They are cornered by three leopard seals. The penguins fight them off and blast themselves off the ship with the egg, causing the ship to blow up. The penguins celebrate their victory by slapping flippers (a "high one"), before the egg hatches. Private (Christopher Knights) is born, and the penguins vow to share their adventures together.

In the present, the penguins launch themselves out of a circus tent while the other zoo animals (Alex, Marty, Melman, Gloria, etc.) are dancing to "Afro Circus", which the penguins are sick of. It's Private's birthday, and the gang decides to celebrate by breaking into the gold supply at Fort Knox. They gas the guards and make it into the vault, only to go past it for a vending machine that produces a banned snack called Cheesy Dibbles, which the penguins are very fond of. Skipper gives Private a gold dollar coin to get himself a bag. As Private does so, he's pulled into the machine. The other penguins get pulled in by octopus tentacles. The vending machine is then pulled up into the sky by a chopper.

The penguins are taken to a secret laboratory in Venice, Italy. It is the lair of mad scientist Octavius Brine (John Malkovich), which is just a disguise to hide the identity of a sinister octopus named...DAVE! He knows the four penguins, even though they have no idea who he is. According to Dave, he was very much loved in his days at the Central Park Zoo, until the penguins were brought there and stole his thunder. Dave was shipped off to every other zoo in the world, only to be upstaged by other penguins. Alone and dejected, he has formed a team of rogue octopi to create a green goo to take down all the penguins in the world. Rico swallows the vial of goo and joins his brothers as they escape the lair. Dave's henchmen chase the penguins across the canal until they hit a dead end. Just then, a snowy owl, a baby seal, and a polar bear subdue the octopi and take the penguins with them on board a high-teach aircraft.

The aircraft arrives at a secret headquarters. The penguins find themselves face-to-face with The North Wind, led by the wolf Agent Classified (Benedict Cumberbatch). The baby seal is Short Fuse (Ken Jeong), the demolitions expert; the snowy owl is Eva (Annet Mahendru), the intelligence analyst, with whom Kowalski becomes infatuated; and the polar bear is Corporal (Peter Stormare), who is the muscle and is also very fond of the penguins for their cuteness. Classified immediately butts heads with Skipper. However, they are also hunting Octavius Brine, unaware of his true identity until the penguins reveal it and also that they have his goo, which is known as the Medusa Serum. Dave then hacks into the North Wind's computer system (while failing to properly get the mic turned on). Dave reveals that he has a whole mess of serum with him. The penguins try and take the North Wind's equipment to go after Dave themselves, but Classified tranquilizes them.

The penguins wake up on a plane that is headed to (you guessed it) Madagascar. They break free from their box, and Skipper presses the bay doors to get them out of there. They fall out of the plane and land on ground with Skipper and Kowalski using Rico to inflate a bouncy house. After spending an hour playing on it, the penguins dig their way to Shanghai (with them mistaking it for Dublin, Ireland). They see on the news that penguins all over the world are disappearing. They deduce that Dave is abducting all the penguins from every zoo in the world that he's been sent to. His next target is there in Shanghai to take the beloved Mermaid Penguins. They mail themselves to Shanghai immediately (and get brought back to the same spot seconds later).

The North Wind learns that the penguins never made it to Madagascar. They head to Shanghai as well. Meanwhile, the penguins sneak into the Shanghai zoo, while Dave is in disguise as Octavius Brine. Skipper has Private disguise himself as a Mermaid Penguin, which only make Private feel bad since he doesn't feel as useful to the team as much as the other three. Private becomes a diversion, drawing the people to him while the penguins break open the sea lion tank to get Dave. Private is then put in the tank with the other Mermaid Penguins. The North Wind arrives in time as the penguins trap Dave under a huge skeleton. However, he escapes through a pipe and drains the Mermaid Penguin tank, taking them and Private. The other penguins are too late to save him. Dave escapes on his submarine. The penguins spot the North Wind's aircraft and hijack it. Eva flies after them while Classified has Short Fuse and Corporal help him chase after them. The penguins, unable to fly the aircraft, accidentally set off the self-destruct sequence, blowing the aircraft up after falling out of it.

The penguins are stuck to a life raft tied to the North Wind's own luxurious raft. They're following Private's signal since Classified put a homing device in the tranquilizers. It takes them to a remote island. Skipper plans a crazy scheme to get in and rescue Private, but Classified has a much more elaborate plan involving their gadgets and walking away from explosions without looking back. Skipper realizes his plan is better and decides it's what's best for Private to be rescued.

Dave discovers that he's captured Private and shows him what the Medusa Serum will do. He takes a cricket and shoots him with a laser that produces the serum, turning him into a hideous monster, which is what he plans on doing to all the other penguins.

While the North Wind infiltrates Dave's base, the penguins create a diversion by wearing liederhosen and entertaining the octopi. Unfortunately, the octopi within the lair capture the North Wind. The other three penguins expect them to bring Private out, but they get captured as well.

Dave straps Private to a chair to use the serum on him while his brothers are trapped and forced to watch. They try to get Rico to cough something up and break out, but Private appears to be zapped and disintegrated.

Turns out he really escaped with a paperclip that he swallowed after taking it from Rico. He then saves the North Wind from getting pulverized in a death machine. Instead of going off to save the rest of the penguins, Classified opts to go back to headquarters to get more equipment. Private attempts to persuade them to stay and fight immediately, because that's what Skipper would do. The North Wind leaves while Private stays to fight back.

Dave brings his submarine to New York City, where a crowd of people are eagerly awaiting the return of the penguins. The octopi activate the laser and mutate the penguins, starting with Skipper, Rico, and Kowalski. Dave emerges in his human suit and presents the penguins before everybody in their mutated form. They terrorize everybody, and Dave tells them to call the exterminators. The exterminators arrive immediately and suck the mutant penguins up. Private then tries to find a way to get through to his brothers. He starts with Skipper, doing a goofy face that always amuses him. Skipper's normal personality returns, and they get Kowalski and Rico to do the same (though Rico is already crazy no matter what he looks like).

The penguins decide that to reverse the effects of the serum, they need something with ultimate cute power, and that would be Private. He straps himself to the laser and uses it on one penguin. It turns back to normal, but it causes Private to grow an arm on his butt. Then, the North Wind arrives in an ice cream truck. They drive it into Dave's submarine, causing an explosion that they walk away from dramatically...only to get caught by the exterminator vehicle. The penguins strap Dave's snow globe collection to the laser, only for the battery on the remote to be low. Skipper sends Rico to the nearest convenience store to get batteries while they continue to fight back. Dave hurls himself toward the penguins, just as Rico returns with batteries and a bag of Cheesy Dibbles. Dave tries to break into the machine to stop Private, but Rico tosses Skipper the Dibbles just as he and Kowalski get sucked into the vehicles. Skipper changes the batteries and launches a Dibble onto the button, activating the laser and turning all the penguins back to their cute and cuddly selves. The effects cause Private to be encased in chrysalis before he hatches again with moose antlers on his head. Skipper tells Private that he is the most valued member of the team. The rest of the penguins and the North Wind all see him as a hero. Suddenly, a rumbling is heard. Dave rises over everybody as a cute octopus...though he just got shrunken and stuck in a snow globe. Skipper throws him to a little girl. Dave has finally found the attention he desired...even if the girl shakes the globe like crazy for the snow.

Classified tells the four penguins that they are the bravest birds he's ever seen. Eva goes to Kowalski and kisses him. The North Wind gives each of the penguins jet packs as gifts. They have fun and fly high in the sky.

During the credits, the penguins find the lemurs King Julien (Danny Jacobs) and Mort (Andy Richter). They use Mort and his cuteness in the laser to turn Private back to normal. Julien then complains that nothing happened to Mort. Mort then swallows Julien whole. Julien is satisfied.

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