Focusing on the ''Madagascar'' penguins and taking place before the events of the first ''Madagascar'', the youngest penguin on the team, Private, slips out of the zoo on Christmas Eve to find a present for a lonely polar bear named Ted. While roaming the streets of Manhattan, he is captured by Nana (the mean old lady from the first film) who mistakes him for a chew toy for her vicious dog, Mr Chew. The other three penguins, Skipper, Kowalski, and Rico, rescue Private from Nana's apartment before it is too late. They escalate into chaos against Mr. Chew, all-the-while, not noticed by Nana, who is occupied watching a American football game. When they are done, they detonate the door with a stick of dynamite (which Rico had repeatedly attempted to use prior), finally attracting Nana's attention and leaving Mr. Chew to take the fall for what the penguins have done to her place.
When Santa and his reindeer crash onto Madagascar it's up to Alex, Marty, Gloria, Melvin, and the penguins to save Christmas.
Valentine's Day is one of Alex the lion's (Ben Stiller) favorite holidays back in the zoo, for he was practically showered with Valentines from numerous admirers, but now that he is in Africa, he is finding that Valentine's Day is not what he was used to.