Ofelia and Philémon are on their way home to Sweden to celebrate Christmas with their grandmother. Their father spends most of his time playing cards in the lounge, so they have to fend for themselves. When their father discovers that rats have gnawed on the money kept in a box in their cabin, the children are promised a reward for every rat tail they can catch. However, the rats—Lucky Closette and Don Calzone—overhear this, and Lucky, a mischievous sewer rat, knows just how to stop them. But how?

Ofelia and Philémon have been shrunk by Lucky Closette, who is now trying to win the Instruction Book from Trassel mé Trunken. Lucky needs the book to steer the ship toward America and warmer climes; she has no desire to go to cold Sweden. After losing time and again, she steals the book and rushes off with her accomplice, Don Calzone, hot on her heels. Trassel mé Trunken sets out in pursuit of the troublemakers. But what will become of Ofelia and Philémon, now that they are tiny?

Trassel, Ofelia, and Philémon have failed to retrieve the Instruction Manual stolen by Lucky Closette. Now Trassel must break the news to Master Estragon—the absolute ruler of the engine room and the person ultimately responsible for the manual. To make matters worse, the Dust Bunnies persuade him to introduce the two shrunken children to Master Estragon, who tends to get very angry whenever Trassel causes trouble.

Neither Lucky Closette nor her shady accomplice Don Calzone can read. That means they can't find the button that stops the ship! By chance, they discover that Ofelia and Philémon can read, and they kidnap the children when no one is looking. But does Don Calzone really want to stop the ship? Or is he mostly helping out for Lucky's sake?

While Trassel mé Trunken and Master Estragon have arrived at the Oil Sump to await the Oracle, Ofelia and Philémon are wandering through the pipelines after escaping from Lucky Closette. They end up in the Storm Bell chamber with the church rat Father Rafael and help him ring the bell to warn of an approaching storm. By the time the Oracle finally appears, Trassel mé Trunken is asleep. But what does the Oracle say to Master Estragon?

Ofelia and Philémon make their way to Trassel mé Trunken and Master Estragon, who are delighted that Lucky Closette cannot stop the ship because she is unable to read. Back at Master Estragon’s place, they try out the telescope he received from the Oracle in the Oil Trough. But there is something magical about it, for everyone sees something different... Just as a Chatter-bat trumpets the news that a ship has gone down in the storm, Trassel spots a lovely little sailor-mouse drifting in a box out at sea. Can they save her?

Trassel mé Trunken becomes a hero when he manages to rescue the cute little Sailor Mouse. Don Calzone is visiting Father Rafael, who promises him a silver tail if he performs two good deeds. Ofelia and Philémon are hungry and want to get back to their dad. Lucky Closette still wants them to teach her to read and scatters some tasty crumbs to lure them over. Does it work?

Ofelia and Philémon are missing. In reality, they have once again been captured by Lucky Closette, who is taking them back to her nest. Smultron-Agnes—whom Trassel mé Trunken had rescued—wakes up among the dust rats and Master Estragon. Trassel is asleep, dreaming that he is with the Oracle in the Oil Trough. In the dream, the Oracle asks him to save them from the scary Bilge-Hog in the engine room; if he succeeds, he will be awarded a hero’s tail. But is it just a dream?

When Trassel mé Trunken mentions having seen the instruction manual at Lucky Closette’s place, Master Estragon isn’t worried at first—after all, Lucky can’t read. But when he learns she has captured the children, he becomes frightened; the children could teach her. That is precisely Lucky’s plan. But will Ofelia and Philémon go along with it?

Trassel mé Trunken takes the compass he received from the Oracle in the oil sump and sets off to rescue Ofelia and Philémon. They are living with her in the sewers, where they receive food and new clothes.

Ofelia and Philémon, who thought the Magic Bottle Cap would make them big, have sprouted tails and ears. Now they are tiny rat-people! To avoid angering Lucky Closette for playing with the cap, they tidy up the sewer. Ofelia even dares to feed the Bilge-Beast. Lucky Closette searches for the Stop Button but accidentally plunges the ship into total darkness instead. How did that happen?

Lucky Closette is not at all pleased to see that Ofelia and Philémon have tidied up her sewer home. To make matters worse, they taught her the wrong letter; after all, you need more than one letter to form a word. Ofelia and Philémon realize that Lucky Closette—who now seems to like them—needs a mate. They decide to catch one! Master Estragon looks through his telescope and wishes he could travel to the moon—that giant cheese. But when Smultron-Agnes borrows the telescope, she drops it! What is it she sees?

Master Estragon is weeping over the stolen Instruction Manual, Trassel mé Trunken, the shrunken children, and the broken telescope. Smultron-Agnes heads into the engine room to search for Trassel and the children. When she slips and injures one of her paws, she receives unexpected help from none other than Don Calzone. Master Estragon meets the Oracle, who gives him a strange medicine. Ofelia and Philémon set a trap for a man and are both surprised and delighted when they see whom they have caught.

The Dust Rats have gathered a heap of items for the recipe Master Estragon received from the Oracle. When they find a blueprint in a note from Smultron-Agnes, Master Estragon realizes that the medicine isn't meant to be brewed, but built! The injured Smultron-Agnes is being cared for by Don Calzone and Father Rafael. Ofelia and Philémon free Trassel from the trap and explain that they tried to use the Magic Bottle Cap to magically grow to full size, and that Lucky Closette is out looking for the Stop Button. Can Trassel now come up with a plan to help the children grow big?

Trassel, Ofelia, and Philémon fly through the ventilation fan—using ice-cream parasols—and land under the bed in the cabin. When their father enters, they rush out and call out to him. However, he sees them as tiny rat-people and thinks he has gone mad. When he starts sweeping the cabin with a broom, Trassel and the children decide it is best to leave, and they tumble back through the fan. What will happen next?