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Kowalski is a ranked as Second-In-Command as Skipper's Lieutenant, Shock Unit (Mr.) Kowalski is the smartest, tallest (if unusually small for his species) and presumably either the second oldest of the Penguins- or possibly the same approximate age as Skipper. Kowalski forms plans for the group and usually takes notes for Skipper. His knowledge has allowed him to take up positions where his intelligence is needed, such as being the team's medic as well as chief scientist and inventor. He tends to unnecessarily over-analyze simple situations.
Kowalski has been in all three Madagascar movies and also in the specials A Christmas Caper and Merry Madagascar. In the first movie, he plays a small role and is only seen briefly at the zoo, then at the Grand Central Station, and afterwards when the team took control of the cargo ship to steer it to Antarctica. When the pengiuns were in the cargo ship, he was navigating for the team, yet he did not get what the map's navigation points were, which is strange for someone like Kowalski.. At the end, he is shown on beach chairs with the other three in Madagascar because Antarctica wasn't that great in their opinion.
In the second movie, he is steering the plane in the cockpit with the other three Penguins, and high fives the other three when they manage to land (Although not so well) the plane, in fact half-destroying it. He is shown to be shocked, along with the others, when blackmailing pictures of Skipper kissing the bobble-head Lola are shown by the monkeys. Afterwards, he is shown again at Skipper and Lola's wedding.
In Madagascar 3, Kowalski becomes even more like his spin-off character - he invents a Warp Drive for the copter and upgrades an SUV with a nuclear reactor to be more easily driven by the Penguins. When it crashes, becoming utterly destroyed, his genius helps to upgrade the circus into a fantastic lights and music-show. Along with the other Penguins he helps to fight off DuBois.
In A Christmas Caper, he is organizing the HQ for Christmas, and follows Skipper and Rico when they go and find Private. In Merry Madagascar, he is hostile towards the reindeer, like Skipper and Rico, although Private falls for Cupid, a young female reindeer. He then flies Santa's sled with the other three after being covered in the magical dust which lets the reindeer fly. After crash-landing similarly to in Madagascar 2, he still high-fives the others and Skipper remarks "Whoever said penguins couldn't fly?!?", and says a similar line in Madagascar 2 after they emerge from the wreckage of the plane. Afterwards, he returns to Madagascar with Alex, Marty, Gloria, Melman, Private, Skipper and Rico although they all wanted to stay in New York.
Kowalski is the group strategist and gadgeteer. He is the brains of the group, known as "the Options Guy," and is sometimes even arrogant or boastful about his intelligence. In fact, he can be such a show-off that Skipper has created the 'Show-Off Jar', which Kowalski must put a quarter into every time he shows off his intellect unnecessarily. He believes that intellect is stronger than brute force (He tries to prove this in The Helmet). While he is certainly the most "book-smart" of the zoo animals, his tendency to over-analyze situations affects how intelligent he appears to the others. He can describe emotions in deep words, but he did admit in Monkey Love that he has trouble comprehending love and expressing his feeling to another, which Skipper knew already. Another example that shows this was in the episode All Choked Up when Skipper , Kowalski, and Private thought Rico was going to be blown up, and he states "I, also, love...you...in the same...way expressed previously...dude." In spite of his hesitant nature, he has proven useful in battles with more intelligent adversaries such as the Blue Hen or Dr. Blowhole (who just happens to be the brother of his love interest, Doris).
Kowalski's main disadvantage is that sometimes, he over-analyzes things, extensive reasoning getting in the way of acting. Also, he can become too fascinated by science; in the episode Jiggles, he becomes almost stark raving mad at the other penguins for not accepting his latest scientific breakthrough/abomination of nature. He called them "science haters" (which made Private sad). It was only when Jiggles tried to eat him that it became a problem.
Kowalski, as a man of science, does not believe in magic or King Julien's so-called sky spirits. However he has witnessed the supernatural and, while he attempts to find a scientific explanation, he doesn't always succeed, such as in Out of the Groove when King Julien had his Groove removed.
Kowalski uses many memes popularized by the internet such as "Wehehehel, fail-ail!" (Night and Dazed), "For the win!" (Invention Intervention), and "Holla!" (Friend-in-a-Box). However, due to his nerdiness, all his attempts to be cool sound rather forced. He also tends to use long words. The others are not always able to understand what he is saying, and sometimes ask him to repeat what he's saying in more simple terms.
Though Kowalski is the smartest of the penguins, he seems to be a little less fit than the rest of the penguins and tires more easily, as seen in A Kipper for Skipper.
He can also be highly sensitive, even a little weepy. He is in love with a dolphin named Doris, tough he has been seen kissing with Eva. It is also strongly implied that he once had feelings for a van and awed "She's beautiful!"; with that, Skipper slapped him. It didn't stop him from gushing over the thing. On the other hand, however, he is shown to sometimes be be very arrogant and condescending, such as in Brain Drain, when, at Private's remark that "Gosh, Kowalski, I think your brain power's already tip top!" he only replies with a deadpan "You also think that there's a little man in the fridge who turns the light on and off."
He also has the worst luck of the four; his inventions always backfire on him and he usually suffers for his arrogance.
Despite the fact that he is the most book-smart of all the Penguins (when he complains about needing to boost his brainpower in Brain Drain, Private remarks that he thinks Kowalski's brainpower is already tip-top), Kowalski is unable to read, which doesn't make any sense at all. However, he seems to have gained a basic handle on this skill in later episodes as he is seen interpreting signs and using the Speak and Spell.
Taken from IMDB
Kowalski is the designated intelligence officer of the Penguin Commandos. As Skipper's second-in-command, it may be assumed that he carries the rank of Lieutenant. Kowalski is always given the most difficult and possibly dangerous tasks, such as planning the subterranean escape tunnels beneath Central Park Zoo, and while he does not always succeed (such as during the navigation of the hijacked vessel), there is no questioning his dedication to each and every mission.
Taken from NICK
When Skipper needs analysis or an immediate invention, Kowalski is there with his crayon, notebook and slightly skewed scientific method. Kowalski's authoritative attitude covers up the fact that he usually doesn't have a clue or unaware about what's happening . Even though Kowalski's a self-proclaimed scientific mastermind, he doesn't read English any better than the rest of the Penguins. Although, on some episodes we have seen him typing on a keyboard for the computer, or his speak and spell, so he appears to read a little bit of English.
- In the episode It's About Time there were three alternate versions of Kowalski. The two other versions came from 2 alternate futures. (they probably share the same consciousness).
- In Brain Drain, Kowalski made himself smarter then usual then (resultingly) hopelessly stupid.
- In The Big Move, Kowalski continuously changed shapes when hit by the Shrink Ray.
- In P.E.L.T., he has an alter-ego of himself, where he's more confident & looks like a military general with a green army helmet & sunglasses & a deep baritone voice.
Kowalski-A is the first alternate version of Kowalski as he came from the original timeline's future & traveled back to the point in time where Private was searching for the Macguffium 239 in the lab, creating the first alternate timeline, Timeline A, Kowalski-A appears to be linked to Kowalski-B, in which, the other alternate Kowalski is Kowalski-A from Timeline A in Timeline B, Kowalski-A has a mission with Private to stop himself from getting the Macguffium or manage to start the Chronotron, Because of his actions, he was forced to make Timeline B upon learning of the time paradox he'd cause, In Timeline A, There are only 2 Kowalskis existing at the exact time as he hides from his doppelganger (Kowalski) to prevent destruction of the universe, Kowalski-A is one of the future Kowalskis responsible for the time rift
Kowalski-B is the second alternate version of Kowalski, he is Kowalski-A as he came from the previous alternate timeline, Timeline A, He creates Timeline B traveling back to the point after Kowalski decides to destroy the Chronotron. His mission is to have Skipper stop his original self & Private & his previous self (Kowalski-A) from destroying the Chronotron, In Timeline B, There are 3 Kowalskis existing at the exact same time, Kowalski-B is one of the future Kowalskis responsible for the time rift he is also now the main Kowalski because he didn't go through the time machine.
This version has an extremely bulbous head from an attempt to supercharge his own brain... and not just literally, as he tends to see no reason to be hard on himself as the possibilities of his new noggin seemed endless from curing the common cold to calculating pi to the millionth digit, and he was able to make flawless calculations for making and perfecting his inventions... at least until the effects began to wear off resulting in an even more stupid intelligence than before the effects.
When the effects of his brain charge worn off, Kowalski's head was so deflated that the white on the front of his head flopped onto the top, giving the bald-spot look (unlike his original, handsome self appearance where he has a widow's peak on his head). In addition, the way he talked sounded like a mixture of King Julien, Mort and Ed from Ed, Edd, and Eddy, maybe even dumber then all three idiots combined, as he couldn't even say the simplest of complex words like "temporary", forgot how to swim, thinks beavers are aquatic birds, and he got a plunger stuck on his face. Despite the stupidity, parts of the original Kowalski's personality seem to be intact, as he likes to help the team on missions (even though being stupid means he does more harm then good) and he seems to find pleasure in pushing buttons on devices ("Listen to me com-pu-ter, I am the boss!"). The old Kowalski was restored when his idiot form got some brain food from eating some "nummy" fish.
Shrink Ray Kowalski
In the Big Move, Kowalski went through several forms by size.
Kowalski was shrunk to at least a millimeter tall. His voice was higher & squeakier. He was in this form three times.
Kowalski was grown to at least 10-12 feet tall. His voice was lower. He was in this form twice
Super Fat Kowalski
Kowalski was eventually shrunk, but was too large. His voice is still the same as when he was Oversized Kowalski, he was in this form once.
Super Thin Kowalski
Kowalski was shrunk back to his original size, but was too small. His voice was in between his Oversized & Shrunken voice. He was in this form once.
Polka dot Kowalski
Kowalski was shrunk back to his original size but this time was covered in multi-colored polka-dots. He was in this form once
Commander Kowalski is an alter-ego of Kowalski that appeared in P.E.L.T.. Kowalski's personality becomes slightly different, he's more confident & has a more ideal way of leading the penguins. He trys not to expose this alter-ego in front of Skipper during Skipper's attempts at P.E.L.T. (only when he knows of Skipper's nearby presence, which he only noticed when they landed near him in the park) Kowalski changes his voice tone so he has a deep baritone that makes him sound like a military leader & wears a green army helmet & a pair of sunglasses.
After he was hit with Dave's medusa serum he got long tentacle like appendences, fangs, and a forked snake-like tongue. He hisses and acts savage until Private manages to get Kowalski's personality to return by telling him that "Eva was talking about him". Kowalski along with the rest of penguin kind was turned back to normal when Dave's ray powered by private's immeasurable cuteness was fired.