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), thinnest 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 where he and the other animals were tranquilized, 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 brains of the team; their group strategist and inventor. He's loyal and usually honest. He's also highly narcissistic - both confident and boastful about his brains and his looks - so much so that Kowalski will regularly try out his completely untested inventions on himself. Sometimes it ends well. And sometimes... it doesn't. He loves to demonstrate his encyclopaedic knowledge of anything and everything, and 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.
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 completely loses it when the other penguins become concerned over his latest scientific breakthrough/abomination of nature, calling them "science haters". It was only when Jiggles tried to eat him that he snapped out of it.
Kowalski, as a man of science, does not believe in unproven 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 popularised 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 lacks the physical endurance of the other penguins, tiring more easily as seen in A Kipper for Skipper. He's convinced that intellect trumps brute force, which brings him into disagreements with Rico.
Despite Kowalski admitting he has trouble expressing his emotions, he still demonstrates strong feelings for others, such as in All Choked Up when he fears that Rico is going to blow up, and by writing bad poetry about a dolphin named Doris - whom he also has a tattoo of. He has been seen kissing with Eva. It is also strongly implied that he once had feelings for a van and gushed "She's beautiful!". On the other hand, in The Otter Woman his main interest in 'Arlene' is scientific as he prepares to study her - while taking her for a nice picnic in the park, of course.
Kowalski has the worst luck of the four, but it's mostly brought on by his own arrogance - his inventions frequently blowing up in his face does nothing to keep him from experimenting on himself, such as in Brain Drain. Even so, he regularly takes hits in other circumstances as well.
Despite his intellect being the highest of all the penguins, Kowalski can no more read than any of them, although for some reason this doesn't keep him from creating complicated equations, which means he is fluent in mathematics and algebra. The writers seem to have realised how this makes no sense at all, and Kowalski seems to have gained a rudimentary handle on literacy as in later episodes he can interpret road signs and use 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 Kowalskis. The two other versions came from 2 alternate futures. (they probably share the same consciousness) and were basically Kowalski.
- 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 & puts on a deep baritone voice.
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.