Submitted by Tornado Dragon
Dave/Dr. Brine turns all the penguins – including Skipper, Kowalski, and Rico – in his submarine into insane monsters with his Medusa Serum-loaded ray gun and brings them before a penguin-loving crowd at Battery Park in New York City, and upon seeing the penguins’ hideous new appearances, the people flee in terror. Dave tells them to call pest control services, knowing that they will dispose of the penguins, and the exterminators soon show up driving trucks armed with vacuums and start capturing them.
Private gets the ray gun out of the sub and into the park, and he finds Skipper, Kowalski, and Rico and helps bring them back to sanity. He then tells them of his plan to reverse the ray’s effects on them and the other penguins by using a source of cuteness, but he reveals that HE intends to be that source when he hooks himself up to the weapon. When Skipper protests this because of how risky it is, Private tells him that now is his time to show just how valuable a team member he is, and Skipper and the others accept his decision. Skipper sets the ray at maximum power while Rico barfs up Dave’s entire snowglobe collection that he earlier ate (the snowglobes come from every aquarium and zoo that Dave got kicked out of because of the public favoring penguins over him), and he and Kowalski put them on the end of the ray’s barrel to act as a beam splitter so they and the other penguins will be turned back in one shot. In the end, despite Dave’s efforts to stop them (and with some brief assistance from the North Wind before they get imprisoned in one of the pest control trucks), the quartet succeed in their task.
As a side effect of being used in the ray, Private is encased in a big egg, and when he hatches, he is covered in a pinkish hue and has moose antlers. Dave is rendered cute-looking from the blast as well but is trapped inside one of the snowglobes, and Skipper hands it over to a little girl who shows great interest in Dave, which makes him happy because someone appreciates him again. Skipper, Kowalski, and Rico give Private his due respect, and the other penguins applaud him. The penguin quartet also gain the respect of the North Wind, and when Classified tells him that he wants to make it up to them for misjudging their competence, Kowalski asks for jetpacks, and he suddenly gets a big kiss from Eva, whom he is attracted to. After Private seconds that request, the North Wind give them the jetpacks, and the penguins use them to fly back to the circus. A few days later, they get a hold of the ray gun, hook Mort up to it, and use his cuteness to restore Private to his old self.
Skipper, Kowalski, Rico, and Private track down Dave/Dr. Octavius Brine to Shanghai Marine World, where he plans to steal the aquarium’s Marine Penguins, and Private is dressed up in the mermaid garb of a Marine Penguin to serve as a distraction while the rest focus on capturing Dave. When Dave shows up in his Brine disguise, Skipper, Kowalski, and Rico ultimately trap him inside a whale skeleton, after which the North Wind arrives and sees what the penguins have accomplished, much to their annoyance. However, when the North Wind attempt to take Dave into custody, he slips out of his Brine getup and down into a drain pipe below him, and through the pipes, he succeeds in kidnapping the Marine Penguins as well as Private. Skipper, Kowalski, and Rico follow Dave through the pipes until they get outside, where they see him caging up Private and the other penguins while escaping on his submarine. They then spot the North Wind’s jet parked nearby and steal it so they can chase after him, and despite the efforts of the North Wind to keep them from taking it, the penguins’ lack of understanding on how to fly it results in them blowing it up with the self-destruct feature, though they get out unharmed beforehand. The North Wind continues the pursuit on a life raft with the penguin trio being towed behind them on a smaller raft as punishment for destroying their jet, and the North Wind eventually get a signal from a homing device they planted on Private (and the others) earlier on indicating that he is on a nearby remote island, which is serving as Dave’s base.
Still in his mermaid disguise, Private is brought into a room on the submarine where all of the other kidnapped penguins are being kept. There, he finds out that the Medusa Serum that Dave developed and put into a giant ray gun will not be used to kill the penguins, but instead turn them into ugly monsters so no one will ever find them adorable again. When Private makes an exclamation at this, he gives away who he is to Dave, and he soon warns Dave that he will never get away with this because his brothers are coming, and together, they will take a wrecking ball to his entire operation. Dave thus announces to his fellow octopi that they can call off the hunt for Private’s comrades and the North Wind because they will be coming to them. That night, as the North Wind, Skipper, Kowalski, and Rico are scouting out Dave’s stronghold, Kowalski remarks that a diversion must be created if they are going to get in and rescue Private. After Skipper and Classified get into an argument over which team will serve as the diversion, Eva suggests that they each present a mission plan, and afterward, everyone will vote on which one they think is better. Classified’s plan clearly proves to be the superior choice, but when Skipper tries to downplay the effectiveness of it, Classified reminds him of how his plan to capture Dave back in Shanghai resulted in Dave capturing Private instead. Thinking about Private’s safety, Skipper tells Kowalski and Rico that Classified’s plan is indeed better, so they will be taking orders from him this time.
The penguin trio do their diversion for the octopi guarding the submarine and lead them away from it, enabling the North Wind to enter it. They storm into the control room and find Dave there, but they get captured moments later by other octopi guards and tossed into cages with the penguins. Skipper, Kowalski, and Rico lose the octopi they distracted, but at the time Classified said he would be out of the submarine with Private, Rico prematurely launches some fireworks in celebration. Of course, the North Wind and Private fail to emerge, and shooting the fireworks gives away their position to the other octopi, so they get seized by them and thrown into a cage as well. They are brought before Dave in his laboratory, who soon shows them that he has Private strapped to a table. Dave aims his ray gun at him, and Private informs his brothers that this weapon will turn them and the other penguins into monsters, not kill them, and Dave interjects to add that he will unleash all of their mutated selves on the streets of New York City. Skipper yells that he can’t shoot Private because he is the “cute one” of their team, so Dave decides to set the ray at maximum power to ensure that Private gets transformed. As Skipper and Kowalski frantically try to make Rico puke up a paperclip that he keeps in his stomach so they can pick the lock on their cage, Dave fires the weapon at Private, and when the light fades, everyone notices that Private seems to have disintegrated.
However, after Dave leaves the room with Skipper, Kowalski, and Rico, we see that Private is hiding under the table, having managed to regurgitate Rico’s paperclip (since he earlier swallowed it himself) and used it to pick the lock on his strap in the nick of time. He then sneaks around the submarine until he sees the North Wind over a monitor about to be subjected to a series of deadly contraptions in another room, so he breaks in, subdues the guard, and shuts the machines off just before the team can get slaughtered. However, as Private heads off in the direction of where all of the penguins are being held, he sees the North Wind going in the opposite direction and stops them, saying that his friends are down the other way. Classified tells him that a massive army of octopi are down there as well, so they are going back to headquarters to get new equipment and come up with a new plan before returning to take down Dave. Private protests, saying that the penguins need their help now. He then accuses them of running away just because they failed once, and Classified says that they are simply regrouping. Private tells them that Skipper wouldn’t care, and whether he had a plan and fancy equipment or not, he would never leave a man behind. Classified remarks that they can’t all be penguins, to which Private replies that maybe they should be. Both parties then continue on in their directions.
Clad in his Dr. Brine costume, Dave arrives in Battery Park in New York City to a delighted penguin-loving crowd since he led them to think that he found all the penguins, and he soon gives the order for one of his henchmen to switch on the ray gun and hit every penguin with the Medusa Serum, which Private helplessly watches from a viewing window. Dave brings all of the mutated penguins out to greet the crowd, and their new appearances initially leave the people terribly confused until Dave tells them to go give the audience a hug, after which the people run away screaming. Moments later, Dave tells everyone to telephone the city’s pest control service, knowing that they will dispose of the mutant penguins, and they promptly show up driving trucks armed with vacuums attached to the front. As the trucks start to capture the penguins, Private breaks out of the sub by driving the ray out through the closed door, and after landing in the park, he exits it to find Skipper. After locating him, he makes him remember how cute he is to snap him out of his insane state of mind, and they find Kowalski and Rico and talk the former back to his true mental state (they didn’t bother with Rico because his mind was pretty much the same either way, though he does remember Private and embraces him). Private soon tells Skipper that he has a plan, and after expelling the Medusa Serum from the ray gun’s chamber, he says he plans to take the ray and reverse its effects on them and the other penguins. After Kowalski points out that they will need a power source of almost immeasurable cuteness to restore them and their brethren, Private goes into the chamber and hooks himself up to the weapon, intending to be that very power source. When they test it out on one penguin and it works, Skipper, Kowalski, and Rico notice that the blast had a side effect on Private by making his butt grow an arm. Skipper orders him to get out because this is clearly too risky, but Private firmly refuses, saying that now is his time to show just how valuable a team member he is. Accepting Private’s decision, the other penguins salute him. Skipper sets the ray’s power to maximum, and Rico barfs up Dave’s entire collection of snowglobes that he earlier ingested (the snowglobes come from every aquarium and zoo that Dave got kicked out of because of the public favoring penguins over him), which are all attached to the end of the ray’s barrel to act as a beam splitter so all of the penguins will be turned back in one shot.
Just as Dave starts to make plans to use the ray gun on other cute animals, he sees the penguin quartet preparing to use it on the other penguins, so he removes his human disguise and orders his henchmen to attack them. When Skipper presses the button to activate the ray, nothing happens, and he sees that the remote is low on battery power. Private thus orders Rico to get some batteries from a nearby convenience store and then orders Skipper and Kowalski to hold off the octopi. Just as the octopi are about to get the better of them, the North Wind drive in, in an ice cream truck, and run over the octopi, then send the truck towards the submarine before jumping out, and the truck crashes into the sub and destroys it. Unfortunately for them, an octopus appears moments later driving one of the pest control trucks, sucks them up into it, and then sends it over onto its side. Dave then launches himself at the ray, and he captures Kowalski after he lands and throws him into a pest control truck before confronting Skipper just as Rico arrives and upchucks a couple of fresh batteries to him. Skipper puts them in the remote, but Dave knocks it out of his flippers before he can switch on the ray. Dave sends Skipper and Rico towards the truck Kowalski is imprisoned in while the remote lands on the ground, then he begins to bust through the glass around the chamber to get to Private. Just before Skipper and Rico can be sucked in, Skipper has Rico vomit up a bag of Cheezy Dibbles to him, and – using it like an R.P.G. – he pops the bag and sends a Cheezy Dibble towards the remote. Dave then gets into the chamber, but Private uses his butt-arm to punch him and send him flying back out, and he lands on the beam splitter. The Cheezy Dibble then hits the activation button, covering all of the penguins with one huge blast and turning them back to normal.
After the penguins and the North Wind get out of the trucks, Skipper, Kowalski, and Rico rush up to the ray to check on Private, and Private undergoes some rapid transformations before finally being encased in a big egg. Corporal smashes the chamber and gets it out, and Private soon hatches out of it alive, but he is covered in a pinkish hue with some polka dots and has moose antlers sticking out of his head. Kowalski remarks to Private that he is disfigured, but Skipper says that, if there is anything that they learned from this adventure, it is that looks don’t matter; it’s what you do that counts, and what Private did was rescue them and all the other penguins. Skipper acknowledges Private as the most meaningful and valued member of their team, and Private shares a salute with him, Kowalski, and Rico before they parade him around on their shoulders while the other penguins and the North Wind applaud him. They then discover that the blast has rendered Dave cute-looking himself, but trapped inside one of the snowglobes, and Skipper hands it over to a young girl who shows great interest in Dave, making him happy that someone appreciates him again (despite the fact that she walks off shaking his snowglobe too vigorously). Classified tells the penguins that they are the bravest agents he has ever known, and he hopes there is some way that he can make up for misjudging them. Kowalski immediately demands that they all get jetpacks, but then Eva comes down to Kowalski and suggests that they should kiss, and she kisses him much to his delight (he had long been holding an ill-concealed crush on her ever since they first met). Private seconds Kowalski’s request, so the North Wind give them the jetpacks, and they use them to fly back to the circus.
In a mid-credits scene taking place a few days later, we see that the penguins are now in possession of Dave’s ray gun, and they hook up Mort to it and aim it at Private to turn him back to normal. King Julien ends up pushing the activation button, and Private is turned back into his old self, after which he and the other penguins walk off to get some drinks to celebrate. Mort shows that he has suffered a side effect himself when he swallows King Julien whole, but Julien finds this nothing short of amusing.