When the Penguins are taken in for injections, Skipper escapes because of the giant needle. The Penguins must now make sure Skipper gets a shot before he leaves the zoo grounds PERMANENTLY!!.
Skipper is calm when they arrive, advising the others to "turn and cough, turn and cough" for a routine check-up. However, Skipper's mood rapidly changes when he finds out they will be getting shots. To show his craziness, the doctor says "Okay, who's my first victim?" While the doctor takes Private, Kowalski and Rico into another room for their shots, Skipper begins freaking out and trying to escape. Before the doctor can come back for him, Skipper knocks the doctor unconscious and escapes through the window.
The zoo staff realizes that a penguin is missing and puts the zoo on lock down. Skipper convinces the other penguins that the zoo is onto their operation, but eventually lets enough slip to draw the suspicion of Private. Skipper admits that he's afraid to get a shot, but agrees to get one so they can stay in the zoo. The others vow to help him through it. However, it turns out Skipper was lying as he disappears when they turn their backs to him.
Private, Kowalski and Rico all chase Skipper through various habitats, eventually coming to the conclusion that he really doesn't want to get a shot. Realizing that the zookeepers are just looking for penguins with an ankle tag, Private comes up with the idea to simply put on Skipper's ankle tag and get a second shot so Skipper will come back. But when Skipper sees what's Private did and explains to Mason and Phil about what's going on, the two chimpanzees explain that getting two shots within such a short time from each other could make Private very ill (or worse). Realizing this, and now greatly worried about Private's safety, Skipper finally decides to just suck it up and get the shot he needs. He rushes to the animal care building, and explains to Private what the chimps told him. As Private leaves so Skipper can get his shot, he assures Skipper that he, Rico and Kowalski won't think any less of him just because he's afraid of something.
Skipper gets the shot he needs and later on, Alice claims that he and the rest of the penguins have a dentist appointment coming up soon -- this makes Kowalski freak out and run away, which causes Private to confusedly state, "But we don't have teeth."