The penguins plan a vacation on the high seas but a storm blows them off course onto the streets of Hoboken, New Jersey.
After being taken to the Hoboken Zoo and meeting some old friends, Skipper is adamant the zoo holds a sinister secret.
Skipper falls into a trap set by Dr. Blowhole (voice of Neil Patrick Harris), who then extracts Skipper's memories and uses them to find the other penguins and transform them into villains. Four musical numbers are featured.
The Vesuvius Twins bring Skipper and Julien to their home and force them to fight one another.
Kowalski creates tiny robots which do the penguins' chores for them, but also grow overprotective of the penguins.
After witnessing a scout perform a good deed at the zoo, the penguins decide to up their good deed quota, however they learn that not all good deeds go unpunished.
Private and Mort are trapped in a vending machine.
While they attempt to escape, King Julian believes they have been kidnapped by TV personality Professor Quimby.
Kowalski finds a way to stop time, unfortunately King Julian gets a hold of his device.
The penguins receive a warning that the notorious Red Squirrel has planted a brainwashed sleeper agent in their presence.
The animals stop receiving special treats from an old woman who may have been injured because of King Julian.
Kowalski is unable to attend a big inventor's expo due to his broken legs.
Private is confronted by Dale the Snail who's determined to take is revenge after Private stepped on him
The Penguins uncover a forgotten device, a giant toilet named Project S.T.A.N.K.
Realizing they must get rid of it, they attempt to transport it to a New Jersey rest stop, however King Julian needs a new throne and decides he wants it.
After Private saves a Leopard Seal from being turned into fish chum, Private agrees to help her get back to Antarctica.
Skipper, Rico, Kowalski & stowaway King Julian must follow him and rescue him before he becomes seal chow.
When the Penguins discover King Julian, Maurice & Mort have been sleeping in the park, they insist they use their secret tunnel so they aren't discovered by Alice.
However when Julian blabs about the tunnel to the rest of the zoo, all the animals decide to move to the park.
The Penguins plan to acquire a feather from an extinct penguin in order to revive the species however, things don't go as planned when they revive an accident prone Dodo bird.
After Kowalski's Love-U-Laser malfunctions, all the animals hate him and want to destroy him.
Kowalski reanimates Jiggles much to the surprise of the other penguins.
Lemmy the robot returns from Mars with a space squid.
Marlene gathers the zoo animals together for 'Game Night', but things that don't go quite as planned when Kowalski, Maurice & Mort go on a snack run that ends in a police stand off