It's been years and years since the Popper family lived in Stillwater, but the town is still riding high on its former residents. Across the river, Nina and Joel Popper have just moved to Hillport with their mother, into a house she got cheaply at auction after the Penguin Pavilion closed overnight. There's a lot to do: unpacking, scrubbing the floors, investigating the basement, which used to be the penguin exhibit -- wait, what's this?! It's two eggs, tucked snugly near the furnace. Penguin eggs! They must have been left behind in the hasty departure.

Nina and Joel come up with a plan. They'll send a message to the caretaker of Popper Island, asking him to come pick up the chicks. But when they go to the port to send the message, the caretaker gives no response. In fact, the seafarer's office tells them, they haven't heard from the caretaker in months.

Setting off on the adventure of a lifetime, Nina and Joel endure perilous storms, a long journey to the South Pole, and penguins. Lots and lots of penguins.