Scene I: Antarctica; a decade before the events of the main films

Narrator: Antarctica, an inhospitable wasteland, but even here, on the Earth's frozen bottom, we find life. And not just any life: penguins. Joyous, frolicking, waddling, cute and cuddly life. Look at them, tumbling onto their chubby bum bums. Who could take these frisky snow-clowns...

As the older penguins almost fall on baby Skipper, Rico, and Kowalski, they move out of the way.

Skipper: Seriously? Does anyone even know where we're marching to?
Penguin #1: Who cares?
Penguin #2: I question nothing.
Penguin #3: Me, too.
Penguin #4: Me, too.
Skipper: Well, fine. We'll just fly to the front of the line and see for ourselves. Kowalski, Rico, engage aerial surveillance.

They flap their wings but cannot fly

Kowalski: Skipper, we appear to be flightless.
Skipper[looks at his wings] Oh, well, what's the point of these? 

Rico seems to have an idea. He hits Skipper's wing in some sort of high five.

Skipper: Woah, I like it! Hey, this could be our thing! What're we gonna call it? Let's call it the, uh... high one.

The egg passes to them

Skipper: Hey, does anybody see that? That's an egg. Is someone gonna go get it?
Penguin #5: We can't do that.
Skipper: Why not?
Penguin #6: Well, it's a dangerous world out there, and we're just penguins.

Skipper: Kowalski, analysis?
Kowalski: We are really... awesome at this!
Skipper: Boys, we did it! Mission accomplished! Hey, we could do our thing! High one!

They all high five, until Skipper accidentally hits the egg they just saved.

Skipper: Oops. My bad.

The penguins all look in awe as the egg is about to hatch.

Skipper: Look, it'’s the miracle of birth!
Kowalski: A moment of extraordinary beauty.

Suddenly, Private's egg explodes open, much to the disgust of the three penguins.

Skipper: Daaagh!! That’s disgusting! I think I have amniotic sac in my mouth!

Much to the surprise of the three penguins, the newly hatched Private gets up, but look at him lovingly.

Private: Hello! Are you my family?

The three penguins turn, knowing that they're far away from land, and nod to each other before turning back to face Private.
Kowalski: You don't have a family, and we're all going to die. Sorry.
Private: Wh-What?

Skipper elbows Kowalski.

Kowalski: What? I thought that was what we were all nodding about.
Skipper: [hits Kowalski] No one's gonna die. [to Private] You know what you got, kid? You've got us. We've got each other. And if that ain't a family, I don't know what is.

Skipper salutes Private, who salutes back. He then tussles Private’s head

Skipper: So adorable. [to Kowalski] Kowalski, what's our trajectory?
Kowalski: Ninety-five percent certain we're still doomed.
Skipper: And the, uh... other five percent?
Kowalski: Adventure and glory like no penguins have ever seen before.
Skipper: I'll take that action.
Private: Where are going?
Skipper: The future, boys. The glorious future.

Scene II: Circus; Present

The song "Afro Circus/I Like to Move It" plays at the circus tent and Marty, Gloria, Melman and Alex's shadow with the wig appears, and they are dancing.

Skipper: Ah, that song! I swear this one is gonna make me lose my salmon.
Kowalski: Singing getting louder, Skipper!
Skipper: Then move faster! Someone get that wig off Private.

Cue Private dancing until Rico removes the wig off him.

Skipper: Kowalski, status report.
Kowalski: I'm really getting tired of this song.

Scene III: Fort Knox

Skipper: Private, if you could have anything you wanted in the whole wide world, what would it be?
Private: Well, gee, Skipper. I think to be a meaningful and valued member of this team.
Skipper: Oh, well, we got you something else.

Camera pans to a vending machine in the break room.

Private: A vending machine?
Skipper: Well, not just any vending machine, Private. The last remaining home in America's nanny houses for the remaining of those succulent and chemically-hazardous bits of puffed heaven called...
Private: [gasps] Cheesy Dibbles!
Skipper: [gives Private a coin] Happy ding-dong birthday, ya little scamp!
Private: Thank you!

In response, Private pecks Skipper on the cheek, followed by Kowalski, finally giving one to Rico, only for the latter to hold Private for ten seconds, before releasing him. Cue Skipper, Kowalski and Rico smiling at Private with satisfaction.

Skipper: You mess with the bull, you get the horns, Private. Now get to that machine and get your present.

Private tosses the coin into the machine and tries to reach in the slot to get the bag.

Skipper: We just broke in the most secure facility in North America. Do you know what that means?
Kowalski: We’re wanted criminals who will be on the lam for the rest of their lives, always feeling the hot breath of Johnny Law on our necks?
Skipper: No. This means as elite units go, we're the elitist of the elite. Top shelf in the bureau. The penultimates. Plus one.

As Private struggles to get the packet out from the vending machine he ends up getting pulled into the machine.
Skipper: Where'd Private go?

They walk over closer to the vending machine.

Kowalski: Oh, there he is.

The penguins notice that Private is stuck up in the machine.

Kowalski: D3.
Skipper: Oh, Private! How much is he?
Kowalski: He's three dollars and fifty cents, sir.
Skipper: Well, that's outrageous. Even for Private.

Suddenly, an octopus tentacle comes out of the vending machine slot, grabs Rico and takes him into the machine.

Kowalski: Sir, the machine is alive!

The octopus tentacle comes out of vending machine again and takes Kowalski.

Skipper[angrily] Well, I don't think I like your attitude, vending machine. Or your prices! [in battle stance] Release them!

Scene IV: Dave's Submarine

Skipper: Kowalski, analysis.
Kowalski: All evidence indicates... [his stomach grumbles] Oooh, I ate too many Cheezy Dibbles.
Private coughs out an orange cloud of dust

Skipper: We're behind enemy lines and incredibly thirsty. Rico, bust us out of these delicious prison.

Rico sticks out his tongue holding a paper clip and uses it to unlock the door.

Skipper: Nice work, Rico. You're a meaningful and valued member of this team.

As the penguins exit the cage, Private becomes upset. Then he looks at the paper clip, takes it and swallows it. He tries coughing it up, but no success.

Skipper: Private, quit lollygagging. And regular gagging.
Private: Sorry.

Skipper: It's dark and ominous. Two of my least favorite traits in a room.
Private: Ooh, look, a button!
Skipper: Huh? Private, don't!

Private pushes the button and the platform underneath them descends and they drop down to another room.

Skipper: Now what have I told you about-
Private: [presses another button] Sorry, what?

A giant ray wheels to them and a laser pops out pointing at the penguins.

Kowalski: It looks like some sort of giant laser sent to kill us all, sir.

Skipper steps back from the laser's angle.

Private: Ooh, another one!
Skipper, Kowalski, Rico: NO!

They stop Private from pushing the button. Suddenly, drops of water comes down on the panel and on the flippers. The penguins look up.

Dr. Octavius Brine: Naughty, naughty. Pretty birds belong in their cages.

He is seen walking on the catwalk, but the camera shows that he is walking upside down. He drops down and his limbs are tangled up. The penguins groan in disgust. The scientist gets himself in that tangled position and screws his head right.

Penguins: Ew!
Dr. Octavius Brine: Now, that's just hurtful. [untangles himself] And I was so happy to see you again, Skipper, [Skipper gasps] Kowalski, Rico, and sweet little Private. [flicks Private's beak] Boop!
Skipper: Who are you?
Dr. Octavius Brine: The humans know me as Dr. Octavius Brine. Renowned geneticist, cheese enthusiast, and frequent donor to NPR pledge drives. But you know me by a different much older name. A name perhaps you hope you'd never hear again. A phantom! A shadow of a former life! I am

A purple octopus emerges from the costume of Dr. Brine.

Dave: Dave!

The penguins gave long surprised looks at Dave with the Dr. Brine hairpiece on his head.

Skipper: Kowalski?
Kowalski: Sorry, sir. No clue.
Dave: [takes off the hairpiece] Dave!!!
Kowalski: Dave...
Dave: Dave.
Skipper: Dave?
Dave: Dave.
Private: Dave.
Dave: Dave!
Rico: Dave.

Dave gives a confused look. A cricket chirp is heard. The penguins look to see a cricket doing the chirp, who then stops.

Cricket: Sorry. [leaves, then stops and turns] Wait, wait. Uh, I live this way. [leaves]
Skipper: Go ahead, Dan, continue.
Dave: You seriously don’t remember me?
Skipper: Dave! Dave! Right! Oh, yeah! Long time! Uh, how’s the wife?

In response, Dave punches the wall behind Skipper

Dave: I’ve never been married!

Dave: The only thing that has kept me going all these years is my burning thirst for revenge...

Skipper and Kowalski are confused.

Dave: ...and my precious souvenir snow globe collection.

It is shown that Rico is swallowing all of Dave's snow globes.

Dave: Ah! What is wrong with you?!
Rico: [mumbles] I dunno.

Scene V: Venice, Italy

Skipper: Alright, boys, battle stance.
Kowalski: [exhausted] We're in battle stance, sir.

Rico takes the sock off Skipper's head

Skipper: Oh, good. Now we spring our trap.

One of the octopi smashes the gondolier's mandolin, who runs away.

Kowalski: I'm not sure they're the ones that are trapped, sir.
Skipper: Kowalski, remember our little talk about true but unhelpful comments?
Kowalski: Yes, sir.
Skipper: Sometimes we just have to wing it.

Before the penguins can do anything. Eva swoops down, grabs one of the octopi and throws him in a window. Kowalski stares amazed.

Kowalski: Wow...
Short Fuse pops out of a light bulb, throws a flash grenade at the other octopus, which explodes, pushing him backwards to the wall. The telephone booth changes shape, revealing Corporal pulling out a taser, shocking the last octopus, who goes through the sewer grate.

Kowalski: Sorry for underestimating the plan, Skipper.
Skipper: It's okay, Kowalski. Just don't ever doubt me again. Now what the heck is going on?

A plane flies over the rooftops and Classified drops down and lands in front of them.

Classified: Remain calm, penguins. You are now under the protection of the North Wind. [shows a badge] You're welcome.

Scene VI: North Wind aircraft

Corporal: Oh my gosh. You guys are so cute! [grabs the penguins and hugs them tightly] And cuddly!
Skipper: Hey, get away! [slaps Corporal's lower jaw] No more hugs!
Corporal: It's like being licked by a basketful of doggy dogs.
Classified: [sighs] Corporal. Corporal! Chart a course back to North Wind Headquarters.

Corporal puts the penguins down, makes a heart sign with his paws before typing a computer

Classified: Eva, inform them we’re bringing in witnesses.
Skipper: Private, dibble me.

Private takes a dibble bag out of Rico's body, gives it to Skipper, then he jumps in front of Classified.

Skipper: We're not going anywhere with you. [munches] We don't even know who the heck you are.
Classified: The North Wind is an elite undercover inter-species...

Skipper munches, Classified looks at him.

Classified: The North Wind is an elite undercover inter-spec... [Skipper munches again] an elite undercover inter-species... [Skipper munches again] task... [Skipper munches again] force... [Skipper munches again] dedicated to help... [Skipper munches again] helping... [Skipper munches again] dedicated to...

Skipper munches again; Classified growls annoyed

Classified: dedicated...

Skipper munches again; Classified finishes his sentence while Skipper is munching.

Classified: dedicated to helping animals who can't [Skipper munches again] help [Skipper munches again] themselves.

Skipper munches again for the last time.

Classified: Like penguins.
Skipper: Really? And you are...?
Classified: My name is classified.
Skipper: Classified, eh? What is that, uh, Dutch? Can't hear that accent.
Classified: Excuse me?
Skipper: There's the accent.
Classified: No, my name isn't "Classified", my name is classified because I am the leader of this straight team. The seal is Short Fuse, weapons and explosives. The bear is Corporal, he’s our muscle. And the owl is Eva, intelligence and analysis.
Skipper: Well, Agent Classified, we happen to be an elite unit too. [accidentally steps on a button which starts an alarm]
Voice: Self-destruct sequence activated.
Skipper: You know, you should really label these things.

Classified pushes the button again, turning the self-destruct off.

Skipper: [shakes Classified's paw] The name's Skipper. I run this outfit. That there is Kowalski, he's the brains of our operation. Say something smart, Kowalski.

Kowalski: [staring awestruck at Eva] Uhhh...

Eva looks back at Kowalski.

Skipper: See? He's working on a whole 'nother level.

Scene VII: North Wind HQ

Classified: What you, of course could not know, is that Dr. Brine's laboratory in Venice is secretly developing a doomsday weapon called the "Medusa Serum."
Skipper: Ah, but what you don't know is that Dirk...
Kowalski: Dave.
Skipper: Dave won't be using his Bazooka Serum...
Kowalski: Medusa Serum.
Skipper: Medusa Serum on anybody.
Kowalski: That part is accurate.
Skipper: Show him, Rico.

Rico spits out the vial containing the Medusa Serum.

Classified: stole the Medusa Serum.
Skipper: Well, stole the serum, saved the day, did your job for you. Call it what you will.

Suddenly, the screen goes on, revealing Dave

Skipper: Debbie!
Kowalski: Dave.
Skipper: Dave!
Corporal: He hacked into our system.

There's no sound on-screen as Dave speaks
Eva: Where's the sound?
Kowalski: Dave, your microphone, it's not on.
Classified: Click on the button with the picture of the microphone.
Short Fuse: Every time a villain calls in, this happens.
Dave: Hello? 

[the screen goes off]

Dave: Hello?
Kowalski: But, now we can hear you.
Short Fuse: So annoying!
Kowalski: But we cannot see.
Short Fuse: Every time!
Classified: It's like talking to my parents.

Dave comes back on the screen

Dave: How about now?

Everyone cheers in agreement

Classified: Yes! That's fantastic.
Dave: Now, where was I?' [starts doing an evil laugh]
Kowalski: Dave!
'Dave: 'Greetings, North Wind. I see you've met my old zoo mates.
Skipper: We were never mates. There was no mating.
Classified: Turn yourself in, David. You're powerless now that I've stolen your precious Medusa Serum.
Skipper: What? You? You didn't steal that!
Classified: It's over.
Dave: It's over? Then why did I call you? Weird. Oh, maybe it was to show you this!

As Dave turns the camera to show the Penguins and North Wind a giant vial containing the Medusa Serum, everyone gasps with shock.
Kowalski: That is a lot of serum for four penguins.
Dave: Oh, you thought this was just about you four? No. No, no, no, no. We're just getting started.

Dave takes a selfie with a camera

Dave: Now, if you'll excuse me, I have to go do some shopping...for revenge!

Dave presses the button to turn off the screen but nothing happens, he presses it again but still nothing happens

Dave: Wait. How do you...? [turns to his octopus thugs for help] What do I push? Is it the red? Or... I thought it was... it's not this...

Dave presses something and the screen goes blank. The picture of Dave in front of the serum comes out of the printer.

Scene VIII: Plane to Madagascar, Sahara

Skipper: Ugh, where the heck are we?
Kowalski: Oxygen content is low. I suggest we limit our breathing.

Then the sound of a fart broke the silence.

Skipper: Aw, Private!

The three Penguins rip holes on the box to breathe for air.

Private: Sorry. I get gassy when I fly.
Skipper: Toot sweet! He does!
Kowalski: We must be on a plane!

The Penguins move the box to be free. Skipper, Kowalski and Rico have darts on their necks and Private has one on his butt.

Kowalski: What did North Wind do to us?
Private: Oh! They gave us badges!

Everyone but Private take off the darts.

Skipper: Not badges, tranquilizer darts! Classified! That low-down dirty dog is trying to kick us off the mission!
Kowalski: He thinks we can't save the penguins because we're just "penguins".
Skipper: Well, penguins are our flesh and feathers! They're us! And if anyone's gonna save us, it's us.
Kowalski: But, Skipper, we've gotta be five miles up. That pretty much limits our options.
Skipper: I make my own options.

Skipper hits a button. The emergency hatch opens and boxes come flying out with the penguins.

Scene IX: Rio De Janeiro, Brazil

Scene X: Shanghai, China

Skipper: Alright, you! Where's Dave? [repeatedly slaps a baby squid] Give us the goods.

Kowalski: Sir, that's a baby squid.

The baby squid starts crying, then Skipper puts the baby squid down.

Skipper: Sorry, laddie.

Scene XI: The Ocean

Scene XII: Dave's Submarine

Scene XIII: Remote Island

Classified: [to Short Fuse] Short Fuse, you were supposed to handcuff them to the raft!
Skipper: [to Classified] Don’t you hologram me!

Skipper turns off the jungle camouflage again, noticing Skipper Short Fuse with Classified.

Short Fuse: I tried, but they don't have hands, they just have flippers, Boss! And I have flippers. So it's flipping useless!
Skipper: All right, pooch. If you won't work with us, you better work for us. Our plan requires a diversion.
Classified: I give the orders around here and as much as it pains me to say this, I need you to act as the die-version for our operation, understood?
Skipper: No. This is our operation and it requires you to cause a diversion!
Classified: Die-version.
Skipper: Deh-version.
Classified: Die!
Skipper: Deh!

Skipper and Classified continue arguing pronouncing diversion, until Eva lands in front of them.

Eva: Gentlemen. There's only one way to resolve this.
Kowalski: We should kiss?
Eva: Planoff.
Kowalski: Yep. Planoff. That's what I was gonna say. Planoff...

Scene XIV: Dave's Submarine

Dave: Oh right. Great catching up. Who’s ready to move into live penguins testing?
Skipper: You point that death ray away from Private right now!
Private: It's not a death ray, Skipper! He's gonna turn us into monsters!
Dave: Yepper-doo! And what comes next, Dave? Invasion! Ahhh! Horrible mutant penguins released on the streets of New York City!
Kowalski: You're the monster!
Dave: [angrily] Yes! I'm the monster. Everyone made that clear to me, every day in my entire life. But now, let's see how much everyone loves you when you’re the monster!
Private: Skipper! Skipper: You can't take away Private's cuteness!
Kowalski: He's the cute one! [Rico grunts in agreement] That's his thing!
Private: What?

Private sighs, as if to say “Seriously?”

Dave: Hmm, you are super cute. We'd better crank this up. Drew, Barry! More power!

Scene XV: New York City, USA

Scene XVI: Dave's Submarine

Scene XVII: New York City

Kowalski: The ray, it works! It WORKS!
Skipper: Private, are you okay?
Private: Yes!

Skipper, Rico and Kowalski gasp in surprise and notice that Private has sprouted a hand out of his buttocks.

Kowalski: Whoa! Butt-hand! There’s a hand attached to his butt. That was not... that was not there before.
Skipper: Get out of there. That’s an order!
Private: [salutes] Permission to defy order.
Skipper: Permission denied.
Private: Then I deny your denial.
Skipper: It’s too risky, Private. It already made you sprout a butt-hand!
Private: I know it has to be me this time. [places his butt-hand on the glass] And I think you know it too.
Concerned about Private’s sacrifice, Skipper places his flipper on the same place where Private placed his butt-hand. They exchange smiles before Private reattaches himself to the ray using his butt-hand.

Private: I’m the secret weapon!