At first, Mrs. Popper was not keen on the thought of having a penguin in the house but she quickly warmed up to Captain Cook - that is, until she noticed that he ate the live goldfish right out of the fishbowl! The Popper's agreed that Captain Cook was a clean, nice bird and they should keep him in the icebox. Mr. Popper decides to create a nest for him in there.

Not long after the repairman left in shock, the police showed up based on a report of a wild animal in the house. Mr. Popper tried explaining that Captain Cook was a calm bird and the police requested he get a permit. Unfortunately, the call down to town hall did not go over smoothly and did not get Mr. Popper what he needed.

Mr. Popper found that it was not easy to take a penguin for a walk. While meandering down the streets, Captain Cook found his way to a passerbyers shoes and started pecking at them. They made their way to the drugstore before two men jumped out of a care to take pictures and interview Mr. Popper. They were making a news story about him.

Upon entering the barbershop, Captain Cook gets into some trouble as he starts 'gawk'ing at the man in the barber's chair. Mr. Popper picked up the penguin and went to take him outside, finding a set of stairs. He recognized that Captain Cook liked sliding down on his belly and, to his surprise, he found himself doing the same thing.

The picture of Mr. Popper and Captain Cook appeared in the newspaper the next day. Strangely, Captain Cook was not acting like himself - no longer being mischievous. They took his temperature and he was way too hot. The family was worried about him so Mr. Popper called the Aquarium and, to his surprise, was delivered a second penguin, a female named Greta, to bring Captain Cook to good health.

Penguins usually only lay 2 eggs at a time but in this case, Greta had 10 eggs and they all hatched. There was now 12 total penguins living in the Popper house! Mr. Popper made a special home for them in the basement, creating a sheet of ice on the basement floor. He also made a swimming and diving pool for the penguins. Although this worked in the winter, Mr. Popper know it would be more difficult come springtime.

With the penguins being trained, Mr. Popper decided he would bring them down to the theater since Mr. Greenbaum, the owner, was in town. He takes them penguins and his family on the bus to the theater where the tries to convince Mr. Greenbaum that the penguins are able to put on an act that people would want to watch.

The final act of the show did not arrive. Mr. Popper suggested that the theater allow the penguins to perform. To Mr. Greenbaum's surprise, the penguins put on a great, three act show! The audience all cheered and Mr. Greenbaum wanted to sign the penguins for many shows in different cities.