Plot
In Antarctica, three young penguins, Skipper (Tom McGrath), Kowalski (Chris Miller), and Rico (Conrad Vernon), rescue an egg from hungry leopard seals and set themselves adrift on an iceberg. From the egg hatches Private (Christopher Knights) and the four become a team. A decade later, directly after the events of Madagascar 3: Europe's Most Wanted, the Penguins depart from the circus and celebrate Private's birthday by breaking into Fort Knox so that Private can buy Cheesy Dibbles, a discontinued product, from their break room vending machine. However, Private begins to feel unimportant to the team. While Skipper is the leader and strategist, Kowalski is the brains, and Rico the arsenal specialist, Private is continually referred to as just being a cute face and doesn't have any remarkable skills.
The Penguins are suddenly kidnapped in the vending machine and flown to a submarine base in Venice. There, the Penguins meet Dave (John Malkovich), a villainous octopus who disguises himself under the human alias of Dr. Octavius Brine. Dave used to be adored in the Central Park Zoo, until the penguins arrived and unknowingly stole his shine. The octopus was then shipped to other zoos but his fame was stolen each time by a penguin shine. Embittered, Dave now wants revenge on the penguins. Rico swallows Dave's snow globe collection along with a canister of green goo, and the Penguins escape. The Penguins are then chased through the canals and streets of Venice by Dave's squid henchmen. Cornered in an alley, the Penguins are saved by the "North Wind", an elite undercover inter-species task force. The group comprises their leader, a gray wolf named Classified (Benedict Cumberbatch), a demolitionist harp seal named Short Fuse (Ken Jeong), a muscular polar bear named Corporal (Peter Stormare), and an intelligent snowy owl named Eva (Annet Mahendru), with whom Kowalski becomes smitten.
The Penguins are flown in to one of the North Wind's secret bases where the agency reveals their purpose is to help animals who can't help themselves and that they've been tracking Dave for a long time, trying to bring him to justice. Dave hacks into the North Wind's communications and reveals to the group he has a lot more of his serum than just the canister the Penguins stole. Dubbing it the Medusa Serum, he aims to use it on all the penguins that stole his fame around the world. Though the Penguins want to work alongside the North Wind, they don't believe the Penguins of being capable allies and tranquilize them, shipping the four on a plane to their "most remote base" (which happens to be back on Madagascar). The Penguins wake up mid-flight and vow to save their species without the North Wind's help.
Ejecting from the plane and landing in the Sahara, the penguins make their way to Shanghai (that they mistake for Dublin) where they learn penguins are already being kidnapped from zoos everywhere. Using Dave's snow globe collection Rico swallowed earlier, the Penguins discover he's going to hit Shanghai next and strategize a plan to stop Dave's scheme. During the plan's execution, Private once again feels unimportant when he is made the diversion. The Penguins' plan works and they capture Dave before the North Wind can. However, Dave manages to escape and succeeds in kidnapping the zoo's penguins, including Private. The Penguins attempt to chase Dave's submarine with the North Wind's high-tech aircraft, but accidentally activate the self-destruct. The two teams track Private with a previously implanted homing device to a remote island. Meanwhile, Dave demonstrates for Private that the Medusa Serum, when blasted in a ray, will turn its target into a disfigured monster physically and mentally. He plans to use it on all of the penguins he's captured so the public will be repelled by their appearance instead of adored.
On the island, Classified and Skipper argue over the best way to stop Dave, but Skipper finally relents when he realizes Classified's leadership is what's best for Private's escape, despite Kowalski and Rico's objections. The Penguins cause a diversion for Dave's guards while the North Wind sneaks in and corners Dave, only to be ambushed. The Penguins are also captured upon realizing Classified's plan failed. With the rest of the Penguins captured, Dave demonstrates his Medusa Serum ray by using it on Private. It appears to disintegrate him at first, but, unbeknownst to the characters, Private managed to escape his bonds at the last minute with a paperclip he had swallowed previously. While Dave sets a course for New York City and corrals his penguins into a large group, Private rescues the North Wind. However, while Private wants to rescue the others, the North Wind plans to flee and return to their base for more equipment before facing Dave again. Despite their attempted persuasion to join them, Private chooses to do as Skipper would and heads back to free the penguins.
Dave's submarine arrives in New York City and he blasts the penguins, including Skipper, Kowalski, and Rico, with his mutation ray. After doing so, he releases them to the people who are terrified with their monstrous appearance and behavior. Private, seeing he is too late, finds Skipper, Kowalski, and Rico, and snaps them out of their disfigured mental state. They deduce that by reversing the ray, they can reverse its effects. However, while Dave had the Medusa Serum, the Penguins would need something incredibly cute. Private opts to use himself as the ray's source of power, accepting whatever effects doing so would have on him. Unfortunately, the remote for the ray runs out of batteries and Dave, discovering their plan, has sent his henchmen after them. Rico heads out to find batteries while Skipper and Kowalski defend against the squids, finding themselves outnumbered. The North Wind returns and destroys Dave's submarine before being caught by a pest control unit called in to take care of the monstrous penguins. Rico returns with batteries and a new bag of Organic Cheesy Dibbles. Skipper just manages to replace the batteries in the remote before Dave knocks it away. Just before being caught by pest control, Skipper sends a single Dibble flying towards the remote and hits the activation button. Having attached Dave's snow globes to the ray to refract the beam, Private's cuteness is harnessed and reverts every penguin back to their original appearance.
However, as the side effects of being used in the ray, Private has been tinted pink and grown antlers. Despite his strange new look, the Penguins show their gratitude and newfound respect for Private. Dave has also been made cute by the ray and stuck in a snow globe where he is admired by a little girl (Angie Wu). Finally seeing one another as equals, Classified promises to grant the Penguins anything they want. In addition to Kowalski getting a kiss from Eva, the Penguins are given their own jetpacks. The four Penguins then fly off above the clouds looking for their next adventure.
In a mid-credits scene, the Penguins return to the circus and plug Mort (Andy Richter) into the ray and use him to revert Private back to normal. Mort doesn't appear to show any side effects from the ray until he manages to swallow King Julien (Danny Jacobs) whole.
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