Episode 1
The penguins are recruited by Buck Rockgut to help him capture the Red Squirrel.
Episode 2
Kowalski travels back in time to prevent himself from building a time machine.
Episode 3
When Roger's sewer home becomes unbearable, the penguins try to find him a new home in the city.
Episode 4
The penguins must protect the zoo commissioner from Frankie the pigeon's wrath.
Episode 5
The penguins try to help Randy overcomes the problems he's having at the petting zoo.
Episode 6
Eggy the duckling is convinced that he can handle dangerous missions like the penguins.
Episode 7
It's a race against time when the whole gang competes with the Rat King to find the Lost Treasure of the Golden Squirrel, which may have a dangerous curse on it!
Episode 8
When the penguins realize their operation is at risk of being exposed, they attempt to destroy the evidence.
Episode 9
The penguins and Julien believe Marlene has cooties after overhearing a group of schoolchildren.
Episode 10
The Amarillo Kid arrives and declares that he has a score to settle with "Mr. Tux."
Episode 11
Private is ready to move up in rank within the penguin commando unit... or is he?
Episode 12
A group of cockroaches ask the penguins for help with their exterminator problem.
Episode 13
The penguins become convinced that a kid on a field trip to the zoo is spying on them.
Episode 14
Private wants to be friends with a group of badgers... until they threaten to hurt Marlene.
Episode 15
When the Penguins send Rico off to help King Julien, an unlikely friendship develops between them.
Episode 16
Julien causes chaos at the zoo when he steals Kowalski's new invention.
Episode 17
The penguins accidentally launch Leonard the koala out of the zoo and into midtown Manhattan.
Episode 18
When animals begin disappearing, the penguins suspect Savio, the new boa constrictor.
Episode 19
Private tells Mort that if he throws a penny in the fountain, his wish will come true... and it works!
Episode 20
Julien goes on a pranking spree when he learns about April Fool's Day.
Episode 21
Rico desperately wants to a voice chip upgrade for his doll-girlfriend.
Episode 22
A puffin from Skipper's past returns and tries to take over the penguins' habitat.
Episode 23
After a series of gadget malfunctions, Skipper orders Kowalski to stop inventing.
Episode 24
When a baby stroller rolls outside the zoo, the penguins redefine the term "daycare."
Episode 25
The penguins' car seems to have a mind of its own after Rico rebuilds it.
Episode 26
Kowalski steals the computer chip from Mort's new video game to finish an invention.
Episode 27
The penguins must stop a contractor from completing repairs on their habitat before he destroys the world!
Episode 28
Two thieves stash a very expensive diamond necklace at the zoo.
Episode 29
When Skipper is knocked on the head, he's unable to lead the penguins on an important mission.
Episode 30
Private accidentally drinks Kowalski's truth serum and starts spilling the penguin's secrets to the rest of the zoo.
Episode 31
When the zoo is closed for Christmas, the animals prepare for "Kidsmas" -- their annual celebration complete with decorations, food, gifts and a visit from Santa.
Episode 32
Julien believes Maurice is plotting an overthrow and the penguins send him through basic training.
Episode 33
Burt the elephant discovers a love for painting, and he's remarkably talented.
Episode 34
Private is smitten with the zoo nurse, but the only way he can see her is to get injured.
Episode 35
The penguins have a plan to beat the heat, but they'll need Alice out of the way.
Episode 36
Kowalski's attempt to super-charge his brain backfires and now he's dumber than mud.
Episode 37
The lemur habitat gets a new resident, Clemson, and Julien loves to order him around.
Episode 38
Private finds a stack of comic books and ignores Skipper's request to destroy them.
Episode 39
Shakespeare in the park has inspired Private as he struts around quoting from the Bard's works.
Episode 40
A simple plan to have Mort spy on the rats ends up with Julien and Skipper captured.
Episode 41
The penguins accidentally blow up the koala habitat wall, so Leonard has to bunk up with Joey.
Episode 42
King Julien and Skipper switch places for a day, troubling everyone involved.
Episode 43
The penguins intercept a fax with catastrophic news -- Maurice has only 24 hours to live!
Episode 44
When Private's cuteness factor tests off the charts, the penguins use it to their advantage.
Episode 45
Annoyed by the lemurs' constant music, the penguins plan to get them moved to another part of the zoo.
Episode 46
The animals panic when a boa constrictor escapes from the zoo.
Episode 47
Kowalski's invention turns Skipper into a baby, so the penguins must find a way to change him back.
Episode 48
The penguins journey to the bottom of the Atlantic for preserved herring.
Episode 49
Private's quirky Uncle Nigel pops in for a quick visit from across the pond.
Episode 50
After a sailing trip to the Massachusetts coast goes wrong, the penguins wind up at the Hoboken Zoo, which turns out to be a perfectly pristine paradise... or is it?
Episode 51
Dr. Blowhole, the penguins' evil dolphin nemesis, returns to New York with a diabolical plan to turn them into creatures of destruction.
Episode 52
The Vesuvius twins adopt Skipper and Julien, then force them to fight each other.
Episode 53
Kowalski invents a group of tiny robots, which he says will protect the penguins from harm.
Episode 54
The penguins are inspired seeing a good deed and decide to perform their own.
Episode 55
Mort and Private are sucked into a vending machine after trying to retrieve a snack.
Episode 56
Kowalski's time-stop invention falls into the wrong hands -- Julien's!
Episode 57
Special Agent Rockgut contacts the penguins with a warning that Red Squirrel has brainwashed one of them.
Episode 58
The animals think Julien caused old lady Gladys to slip and hurt herself.
Episode 59
Kowalski is laid up in the hospital, so he can't attend the invention expo, and it's driving him crazy.
Episode 60
Private accidentally steps on Dale the snail, so Dale wants some payback.
Episode 61
Julien becomes enamored with the gigantic toilet that the penguins built, but it's all a trap!
Episode 62
Private's heart overcomes his instinct to flee as he helps a stranded seal get back to Antarctica, and the rest of the team follow in the submarine to make sure they make it.
Episode 63
Julien is supposed to keep quiet about the penguins' secret tunnel, be he blabs anyway.
Episode 64
Kowalski tries to bring a penguin species back from extinction, but clones a Dodo instead.
Episode 65
Skipper orders Kowalski's love ray to be put in reverse.
Episode 66
When the penguins discover that Jiggles is still alive, the others start squishing it, which makes it multiply.
Episode 67
Lemmy the robot returns from Mars with a space squid.
Episode 68
Marlene plans a game night to help the zoo animals bond but it takes a terrible turn when the snacks run out.
