The movie starts off with a young boy speaking on the radio with his father, who is some sort of explorer who is constantly travelling around the world.
This scene is repeated as the father calls in from various destinations.
Years later, the small boy has grown into a smooth, fast talking businessman, known as Thomas Popper. His job involves persuading clients to sell their property to his company. Together, with his personal assistant, they attempt to win over a client who is unwilling to sell his property by Popper sharing with him an anecdote of how his explorer father discovered the Horn of Africa or some location like that. The client, who was previously reluctant, now agrees to sell the property.
So, Popper is apparently a very successful man with a big apartment and all; however, he has bigger aspirations of becoming a partner with his firm. The bosses are willing to grant this, but there is one catch - Popper must be able to convince the owner of Tavern on the Green, a building which contains a restaurant, to sell the piece of property to the company. Popper, having full confidence in himself, takes on the challenge.
Somehow, we discover that Popper is a divorced man with two children, Janie and Billy. He visits them every alternate weekend. On one visit, Janie refuses to go home with him as Popper is a detached father who doesn't understand her "boy problems". He leaves without his children, and proceeds to visit Mrs Van Gundy, owner of Tavern of the Green, who to put shortly, does not want to sell it until she finds a person "worthy" enough to sell it to.
One day, Popper receives a wooden crate from his father (who died recently) containing a frozen penguin (he doesn't know this yet; he assumes it's a statue or ornament of some sort). The penguin defrosts and poops on his shoe. Needing to get to work, he sticks the penguin in a bathtub with some ice and leaves it alone in the bathroom. When he goes out, he trips on the crate, smashing it. This causes a letter which was attached to the crate to accidentally slide under a cupboard, so Popper doesn't know that there was a letter.
Anyway, he goes off to work. Meanwhile, the penguin has somehow managed to turn the tap on, leaving the bathroom to flood, to the point where the bathroom becomes an aquarium of sorts when the water floods to ceiling. Popper returns, and opens the bathroom door, sending a gush of water to pour out. As the bathroom is on the second floor, when the torrent of water gushes out, it pushes Popper to the first floor. Popper has had enough of this and calls various animal collection authorities to pick up the penguin, but to no avail, for these organisations are by law, unable to take in such animals. Popper then calls the person who was authorised to send him the penguin to send another crate so that he can send the first penguin back.
Some time passes. It is his son's birthday and the family, including his ex-wife and children, are coming to his house. Popper is busy wrapping up presents. Meanwhile, the penguin, which is watching TV, sees a wildlife documentary about eagles soaring through the sky and pathetically imitates it by flapping his wings. (important later). Popper, being evil, switches channels when he notices the penguin enjoying the programme.
Meanwhile, the empty crate (so he thinks) arrives. He opens it, only to discover that there are five more penguins. They run amok in his house. Just then, his ex-wife and children arrive. His son mistakenly thinks the penguins are his presents and declares them the "best birthday present". Just then, Nat Jones, an official from New York Zoo, comes to collect the penguins. However, Popper realises that his son and daughter are enamoured with the penguins and asks that they be collected some other time. Nat Jones agrees and leaves, but not before saying that the conditions in Popper's house are not suitable for rearing penguins.
As the earlier deal with Mrs Van Gundy has failed, Popper wants to try to win her over by attending some sort of soiree at the Guggenheim museum. However, the penguins need to be babysat. It was discovered that their attention can be captured by screening Charlie Chaplin movies, making them very obedient. Popper tells this piece of information to the babysitter he hired. He leaves. The babysitter is at first very surprised at their obedience, but then, she sits on the TV remote which then changes the channel into a documentary about frightening seals. The penguins are horrified, and their calm facade dissolves into chaos. This horrifies the babysitter, who runs out of the apartment, leaving the door open. The 6 penguins escape, somehow making their way to the Guggenheim museum. Meanwhile, Popper once again fails to seal a deal with Mrs Van Gundy. He is shocked to discover the 6 penguins at the museum. He rushes to the first level of the museum. The penguins attempt to follow him. Knocking over a man with an ice bucket, they slide down the spirals of the museum until they reach the main ground. There, they crowd around Popper, who then flees the area.
As time passes by, Popper has a growing sense of attachment to the penguins, who has been helpful in bonding with his children. The penguins then start to lay 3 eggs. He becomes a devoted caretaker, going so far as to transform his house into some sort of winter wonderland by shovelling snow into his house. For a period of time, all is well. (somehow, we don't hear about his failure with the Tavern on the Green). He asks his ex-wife on a date, and they go on a date at the Tavern on the Green. There, he tells her a story of how on the (infrequent) times his father returned, he would bring him to the Tavern to open his presents. It is a nice memory that he has of his father.
Soon, the eggs start to hatch. However, the last one refuses to hatch. He calls in Nat Jones, who is some sort of expert on penguins, who claims that because of the "improper" care the penguins have received, the egg doesn't hatch. This causes Popper to feel much guilt and thus, releases all the penguins to the care of New York Zoo. This comes shortly after a scene where Popper's bosses come to visit him, see his snowfilled abode, think he has lost a few screws in his head and promptly fire him.
However, Popper soon jumps back into his old life, by waltzing into his office, pretending that all is normal. The bosses decide to take him back. His children who come with him are all very upset that the penguins are gone, and their old resentment (which had disappeared because of the penguins) come back. Soon, however, it is announced that Mrs Van Gundy is having an announcement at the Tavern. The bosses think that this is where she will announce her decision to sell the Tavern. Popper is supposed to turn up for the event. However, he makes a quick decision to get the penguins back as he realised that they meant a great deal to him. Together with his children and ex-wife, they rush to New York Zoo. There, they're informed by Nat Jones that the penguins are ready to be transported to another zoo as New York Zoo already has penguins. Then, they hear sounds coming from a walk-in ice room which contain the penguins. There, they lock the Nat Jones in it and attempt to escape. They sneakily walk through a gift shop where the last penguin gets entangled in a kite that the shop is selling. Somehow, the entire family (with the exception of the last penguin) make it past the gates. The last penguin flees to the top level of the zoo, but Nat Jones, who has escaped from the ice locker informs Popper that he has the last penguin. Popper is horrified to hear this, but then sees the last penguin being confronted by the zoo staff. The last penguin chooses to hurl himself down. Just at the right moment, the kite entangled with the penguin spreads out and it is able to swoop and fly down to the safety of the getaway vehicle. There, they rush to the Tavern, where Popper asks Mars Van Gundy not to sell the Tavern. She says she was not going to, but after seeing the devotion he has for his penguins and family, she realises that he is indeed worthy, and offers to sell it to him. He refuses, but in the end, the Tavern is reopened but its decor is improved.
Lastly, the entire family makes a trip to the Antarctic to return the penguins and everyone is happy.
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