The episode takes place half a year after "Dr. Blowhole's Revenge."
Skipper arrives in Shanghai, China on a super secret solo mission that leads him waddling right into Hans and Dr. Blowhole's trap. Without his men (who are back at the zoo), his memory gets wiped away by Dr. Blowhole's “Mind Jacker.” The dolphin was using Skipper's memories to locate their HQ and fire his "Diabologizer" at Kowalski, Rico and Private to turn them into evil creatures of destruction.
Skipper washes up on a deserted island of Madagascar and goes through two spirit guides (one being Buck Rockgut) before meeting his third and final spirit guide Alex the lion. Alex helps Skipper avoid the Arch Enemy Seeking Missile by dancing and with his help, Skipper regains much of his memory (of snow cones) and sets sail for Manhattan.
King Julien's new MP3 Player's batteries had died, leading him to try and steal Kowalski's Experimental Power Cell. Kowalski takes his invention away (most likely to hidden level 13), but Julien sneaks in at night to retrieve it. The deed was done when he went back up to the main level, only to have Blowhole's Diabologizer fire at his player (saving the three penguins in the process). The player begins to grow and mutate into a mechanical monster which eventually envelops the zoo in a energy field. Putting anyone within its radius under mind control that forces them to sing. and using a sonic blast from its earphones to attack anything that sings off key.
Skipper and Alex wash up in Manhattan, just not New York. As they make their way back to the zoo, Skipper grows more and more annoyed at his spirit guide's inability to shut up and that makes Alex more annoyed and exasperated of Skipper not listening to him. He finds a way to make him disappear, but later ends up in the wrong zoo: The Bronx Zoo. Alex reappears and points him in the right direction.
Back at Central Park, thBronx Ze zoosters are panicking at the sudden attack. Kowalski explains the situation (with help from Blowhole) through song as the player tries to blast them. Blowhole quickly devises a brand new plan and sings a porpoise power ballad to the monster, all about how he wants to use the monster to take control of the city. The monster is taken by the song and willingly allows Blowhole to control it. With the beats at his flipper tips, he sets off for midtown, destroying everything in his path.
Skipper reunites with his team and Kowalski explains the situation. They decide that Julien would be best bet at beating Blowhole, and he distracts the player while the penguins try to stop him (Blowhole). The penguins fail, and Alex gives Skipper a hint as to what he should do. Skipper then sings, eventually finding his rhythm, and they defeat Dr. Blowhole by extracting Kowalski's power cell while he was distracted.
With Blowhole thwarted, he tries to escape, but Skipper activates his Mind Jacker on its owner and wipes his memories. In the end, Blowhole has been sent back to Coney Island as Flippy the Dolphin, once again forced to jump the ring of fire.
In the end, Skipper thanks Alex for helping him, does an imaginary high-five, and Alex disappears.
- "What the Heck is That?" - Central Park Zoo zoosters (minus the Penguins, King Julien, and Mort)
- "Julien's Music Player" - Private, Kowalski, Rico, King Julien, and Mort
- "Everybody Must Sing" - Kowalski and Dr. Blowhole, the Central Park Zoo zoosters
- "Brand New Plan" - Dr. Blowhole
- "Porpoise Power Ballad" - Dr. Blowhole, the Lobsters, Private, and Kowalski
- "What the Heck is That?" (reprise) - Driver, Kowalski, and Skipper
- "Thump Thump" - King Julien
- "We Are the Penguins" - Skipper and Alex
- "Skipper Blues" - Skipper, King Julien, Private, Rico, Kowalski, and Dr. Blowhole