The other three penguins soon recognize Rockgut's errant paranoia and get him to leave by telling him the real Red Squirrel was in a made-up place called "Grrfurjiclestan".
Skipper then tells the other penguins about how he had failed to act under similar circumstances when the previous commissioner had been attacked with bird droppings containing blueberries, vowing to not let the same happen again.
One century ago, the Golden Squirrel places the key to a hidden treasure into a time capsule to be buried in commemoration of the opening of the Central Park Zoo.
When the time capsule is opened in the present day, the race is soon on between the penguins, lemurs, Marlene, and Fred to reach the legendary treasure before King Rat and his minions do.
When the animals return to the zoo and discuss their adventure, a pigeon comes by and asks Private to guard a crystal feather, but everyone but Skipper soon disperses, not wanting anything to do with another ancient mystery.
Special guest star: Debbie Reynolds as Granny Squirrel Private is distraught when cockroaches appear in the HQ, taken in by Rico when threatened by an exterminator.
Following a long stakeout, Officer X, now an exterminator, arrives on the scene, and soon manages to tie up Skipper, Kowalski, and Rico as Private slips away.
To save his teammates and defeat X, Private temporarily suppresses his feelings of disgust and covers himself with numerous roaches, which crawl off him and into X's clothing when the lights are turned off.
After the penguins' short mission to recover a wild Marlene from the park after she had accidentally been knocked into it, Private learns that the zoo had acquired a badger exhibit.
While there, Leonard is accidentally launched from the now-overhauled HQ evacuation system and touches down in Midtown, provoking the penguins to set out to find him and bring him back to the zoo.
Shortly thereafter, when Mort goes missing, the penguins confront the boa, Savio, to see if he had any role in the disappearance, but it is apparent from the configuration of his habitat that he had no means of escaping the enclosure.
Later, when Maurice and Marlene go missing, the penguins continue to suspect Savio of eating the small mammals, and soon send Private out as bait, dressed as a monkey.
When he disappears, the other penguins and Julien confront Savio once again, whereupon he breaks free from his enclosure by sending his tail through a ventilation shaft and deactivating his habitat's electronic locks via a keypad.
Meanwhile, as the lemurs hunt for a tree before ultimately stealing one akin to the one in Rockefeller Center, chaos ensues at the zoo between different groups of animals over whether decorations should be rock and roll-themed or Dickensian.
Special guest star: Carl Reiner as Santa Claus When Burt gets a hold of Alice's paintbrush, he paints a picture of an elephant with it on a nearly wall to the delight of zoo patrons.
Not wanting to lose his friends, however, Private pretends to have avian insanity fever in order for Shawna to treat him like the rest of the penguins (including the painful injection).
At night, however, the others secretly view the comics and then decide to act as a superhero team (Private as "Steel Penguin," Kowalski as "The Throbbing Cerebellum," and Rico as "Barf Bag"), foiling minor inconveniences throughout the zoo.
After learning of Savio's escape from Hoboken on a TV news report, the penguins organize an effort to protect the zoo from the vengeful boa after he took out Burt.
Skipper is pleasantly surprised when Julien begins talking tough about fighting Savio, and partners with him as the group prepares the zoo for battle.
Soon, the team is greeted by friends and enemies Lulu, Hans, Savio, Clemson, and Rhonda who cheerfully welcome the penguins to Hoboken and tell them about Frances, a new zookeeper who has made their lives enjoyable, including by letting them use massage chairs.
When Frances meets the penguins, she is equally as cheerful, though Skipper maintains that she is a "dark mastermind," even as his teammates begin to take a liking to Hoboken.
Special guest star: Megan Hilty as Frances Alberta, Jane Leeves as Lulu, Kathy Kinney as Rhonda, Larry Miller as Clemson and Nestor Carbonell as Savio Note: This is a half-hour episode.
To aid in helping him regain his memory, Skipper's mind hallucinates a "spirit guide" for him to follow in the form of Alex, a lion who had once been a Central Park Zoo neighbor.
With the power cell inside, the Diaboligizer's ray hits it instead of the penguins, resulting in the device increasing in size, floating in the air, and creating an energy bubble which causes the whole zoo to speak only through song.
Blowhole manages to exploit this development by singing to tame the mutant MP3 player in order to take control of it and then leaves the zoo with it to unleash his wrath against the city.
Kowalski unveils his latest invention: "nanites," tiny robots which are capable of operating any mechanical object, thus freeing the penguins of time spent on chores.
Hunter, a young leopard seal pup, is accidentally brought to New York inside the fishing nets of Antarctic poachers Cecil and Brick.
Though Hunter presents herself as a non-penguin-eating "fishetarian," the others fear her predatory instincts and decide to help her only as far as launching her from the HQ into the East River with the instruction "go south".
Dode is then cloned repetitively, only to manage to get himself killed through various reckless actions each time, which Kowalski attributes to dodo DNA having evolved to lack fear genes through centuries of having no natural predators.
These final Dodes then recklessly kill themselves, except for one which the penguins manage to save by daring him into having a staring contest with a taxidermied dodo at the museum, which he begins doing for perpetuity.