Popper does everything he can to help Captain's egg hatch - and loses his job in the process, but finally must call in the experts at the zoo. The zookeeper shows up, and happilly takes the 6 penguins and 2 new chicks away.
Popper returns to work with a plan to get the Tavern on the Green sold. The team are glad to have the old Popper back.
The kids are distraught when they see that the penguins are gone, and Popper finally realises that they are right when he finds a note from his father. Popper picks the kids up in a limo - he gives good advice to his daughter, and is told to give in to his feelings and call his ex-wife before she leaves the country. He offers her a second date - at the zoo.
She accepts and they all meet together - but the penguins are nowhere to be seen. They confront the zookeeper, to hear that they have been sold to different zoos. They hear a squawk from the office, and open a freezer to find them hiding. They throw the zookeeper inside and break out the penguins -- through the gift shop and out the zoo. They wear masks to keep away zoo guests, but the zookeeper is out and tries to stop them.
Pip causes a disturbance, and they manage to get out the gates - but Captain has been left behind - caught up in a parrot kite from the gift shop.
They can only watch while Captain is chased to the roof - but then she jumps and the kite expands - she floats through the air, and lands inside the limo. Popper traps the zookeeper's hands in the gate, and they're off.
They get to the auction and stop Mrs Van Gundy before she sells. The zookeeper shows up, again, and Pip can't stop the penguins waddling inside. In a final test - the zookeeper makes the penguins choose between him (and some fish) and Popper. They choose Popper.
The zookeeper threatens to phone the Mayor - but Mrs Van Gundy does it for him. Popper admits that he loves the penguins - and also he doesn't want the Tavern to close as he used to go there with his father. Mrs Van Gundy has always remembered him. She sells - to Popper. He refuses to tear it down. The zookeeper is escorted outside by the cops - and Pip meets a guy who likes his "Q"s as much as she likes her "P"s!
Later, Popper returns to the Tavern and everyone is there - he takes the table near the window with his family, and they plan a holiday.
As it ends, they escort the penguins to the Antartic, and are happy to reunite them with their families. Captain lays another egg.