The story continues from the events of the second film, Alex (Ben Stiller) has a nightmare about them still stranded in Africa and finding they have all have gotten old. Awaking from his dream, Alex suggests to Marty (Chris Rock), Melman (David Schwimmer), and Gloria (Jada Pinkett Smith) that they should go to Monte Carlo to get the Penguins to fly them back to New York City, which everyone agrees.
In Monte Carlo, the Penguins and two chimpanzees, Mason and Phil (disguising as the King of Versailles) keep winning in gambling until Alex’s gang’s attempt to reach them blunders and sparks chaos in the Hotel De Paris. Hotel security calls Monaco Animal Control officer Captain Chantel DuBois (Frances McDormand) to deal with the animals, but she wants them, including Alex, dead as trophies. During a high-speed chase between the relentless DuBois and the animals in a truck driven by the Penguins to reach their aircraft, the animals barely manage to elude her.
In the skies of France, the plane’s engines fail again and it crashes into a suburban train yard with the authorities closing in. Seeing their only chance of escape is on a circus train, the four desperately claim that they are circus animals themselves, which convinces circus mates Stefano the Sea Lion (Martin Short) and Gia the Jaguar (Jessica Chastain) to let them in. The animals soon learn from Stefano that they are performing in Rome andLondon, where they plan to impress a promoter to get them on their first American tour. Before the zoo animal’s claim is discredited, the penguins suddenly appear with an offer to purchase the circus themselves, resulting the pleased departure of all the human staff. Meanwhile, Julien (Sacha Baron Cohen) falls in love with Sonya the Bear (Frank Welker) and goes on a city tour across Rome while the others are preparing for the performance at the Roman Coliseum. To the Zoo animals’ horror, the circus proves so inept that the angered audience demands refunds to the point of chasing the circus to the departing train to London.