After a vacation to the Massachusetts coast goes wrong, the penguins find themselves at a surprisingly clean Hoboken Zoo, but something is clearly going on behind the scenes.
The penguins set off on a sailing trip to the Massachusetts coast, but bad weather abruptly tosses them onto the streets of Hoboken. There, the team is quickly noticed by humans, boxed, and brought to the feared Hoboken Zoo.
Back at the Central Park Zoo, Mort becomes exhausted trying to get a response from the holographic versions of the penguins and collapses. King Julien arrives on the scene, angry that Mort is bowing down to something that isn't his king. He then repeats Mort's actions trying to wave to the holograms until Maurice turns them off. Though fearing that something unspeakable has happened to his neighbors, Julien decides to take advantage of their absence to commandeer their TV.
Meanwhile, the penguins dread going to the Hoboken Zoo. But the sight that greets them there is not the wasteland they had expected; instead, the zoo is pristine. Soon, the team is greeted by a friend and enemies Lulu, Hans, Savio, Clemson, and Rhonda who cheerfully welcome the penguins to Hoboken. After giving out a song depicting the paradise of Hoboken, a naturally skeptical Skipper starts whacking all his enemies until his team restrains him. The Hoboken animals assure him that the zoo has changed and tell them about Frances Alberta, a new zookeeper who has made their lives enjoyable, providing fine cuisine, massage chairs and even a cheese fountain. 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.
Out of desperation, Skipper regurgitates the "Hoboken Emergency Hollow Tooth" and activates it. Back at their HQ, clear directions to Hoboken are given along with a loud alarm siren, but Julien ignores all of it and when Maurice asks if they should do something, Julien chews up a peanut butter winky and spits it into the loudspeaker in annoyance because that "fixed" the problem, as he couldn't hear the TV. He then becomes excited when his favourite program, the Nonstop Dance Boogie Network, comes up. But he despairs when German polka music is played, his "booty's" one weakness. And worse, he can't find the remote. Therefore, on Mort's suggestion, he decides find the penguins. Though Maurice suggests they go to Hoboken, Julien decides to first slam Mort in a toy store before actually going to find the penguins.
As the penguins are made roomies with Hans, a paranoid Skipper has his men look for any possible conspiracies surrounding Hoboken. But it becomes apparent that nothing seems to be wrong in Hoboken, which Skipper soon begins to agree with. The truth is finally revealed, however, when Frances throws Skipper down a chute into an underground cave where he meets his teammates and the real Hoboken Zoo animals.
Kowalski explains that Frances had used a DNA scanner in the massage chairs to copy each animal's DNA so she could create bio-mechanical android doubles because of her obsession with keeping things clean and deems the real animals unsanitary. As Skipper chews everyone for falling for Frances' deception and getting massages, they are all confronted by his android duplicate (he confesses that he went for one back rub), who punches Skipper up through the drop chute. This gives Kowalski the idea for Savio to swallow everyone but Rhonda, who then fires him like a slingshot to the surface, where he regurgitates everyone (Rhonda joins them all later). Soon after, the real animals and the androids confront each other as a press conference to honor Frances' work is held by the park's commissioner Pervis McSlade. Worse, McSlade intends to give Frances jurisdiction to handle Manhattan, which Skipper fears that she will replace all of Central Park Zoo's animals; though he could live with the thought of the Julien-android punching the real one. Skipper leaves to stop the handshake (which works as a contract) but is caught by his own double. Just as he is about to strike, the lemurs jump on the scene, pinning the android down with a sewer hatch. King Julien demands to know where Skipper had put the remote for their TV, to which he easily answers.
Skipper traps his double between two of the massage chairs and turns them up to the maximum power, the resulting explosion causing them both to land right into McSlade's hands just as he was about to shake Frances's hand. Seeing all the animals causing chaos and making messes, Frances bursts into a fit of rage over the "filthy animals" and attacks them with a broom. Skipper stops her and kicks her into a trash bin. A furious McSlade summarily fires frances and had his guards take her away.
As the penguins jump into the fight, they agree that this was the perfect vacation as wait for fight some more. Back at Penguins HQ, the lemurs get tired of watching the fight and switch channels, only to switch back to the German dancing channel, much to Julien's displeasure. Julien throws Mort to the TV and turns it off as the episode ends.