Four confused penguins named Skipper (the leader of the group), Kowalski (the smartest of the group), Private (the youngest of the group) and Rico (the craziest of the group) continue there epic journey and embark new adventures. They live at Central Park Zoo of the busy streets of New York; they also try to keep their multi species happy. But one day a party animal moves next door named Julien King of the Lemurs, and now all is not normal.
Every year, Private is chosen as the cover animal for the zoo brochure, but this year the photographer discovers the adorable Mort. Bada and Bing offer to, ahem, get Mort out of the picture. And when Mort actually does disappear, Private is torn between his desire to be the zoo cover model and his good heart.
When a beautiful female falcon lands in the zoo with a broken wing, Skipper falls for her and insists she stay to recover at the zoo until she can fly again. The falcon, named Kitka, thinks Skipper is handsome and brave, so she agrees to not eat any of the other zoo animals. Skipper and Kitka are then shown going on a date and they fall in love.
Kowalski creates a living blob of green gelatinous matter after a night of working in his lab, which soon develops a taste for fruit and a hatred of fish. When the blob, which Kowalski names “Jiggles,” begins to increase in size, the other penguins begin to get concerned, but Kowalski continues trying to bond with the material, including after it breaks out of the HQ.
“Mother Duck” and her ducklings discover a monstrous snakehead fish living in their pond. They ask for the penguins’ help getting rid of the deadly fish, which the penguins try to accomplish by building a submarine. Everyone except Skipper is afraid of the fish, so when the submarine gets stuck in an old tire, Skipper goes outside to untangle it and is swallowed by the giant fish in the process. The remaining penguins, under Kowalski’s leadership, forge ahead to avenge Skipper.
After waiting alone for visitors to come to the zoo, Skipper finds the other penguins watching the “Dumb Animal Channel” Rico discovered on TV. Skipper takes a peak at it, and he soon gets addicted, too. Marlene appears and tells the penguins that the zoo is closing forever. The five animals investigate and find plans to what is happening. They tell all the zoo animals that if there are no more guests, they will be shipped out all over the world. Mason pulls out a camera he took from the lost and found and suggests they make a commercial promoting the zoo to be broadcast all over New York City.