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Ten-year-old Jan and Malaysian eleven-year-old Adinda, who were both orphaned during World War II, are walking home to their foster parents one day when they rescue a dog from an old man. While stern Mother Grijpma, the children's foster mother, refuses to accept the new animal, Father Grijpma, the pastor of the small Dutch village of Niewerland, allows the children to keep the dog. Naming him Bussy, they secretly house the dog with their other pets, Ko the rabbit and Noisette the cat, in the church belfry. One night soon after, when a severe wind storm causes floods that threaten the dikes, Officer Peiters asks Father Grijpma to ring the church bells to warn the villagers. Rushing the children to the belfry, Father Grijpma orders them to ring the bells, then promises to return with Mother Grijpma. Still alone hours later, the children fall asleep huddled with their pets, as the storm winds howl outside. The next morning, Adinda and Jan look out the belfry window onto their village, which is immersed in rising waters. While Adinda cries that all the villagers are dead, proud Jan refuses to believe her until they see Mother Grijpma's corpse floating by. Noticing that an abandoned houseboat has moored to the church, the children climb over the roof tiles with their pets, including Prince the rooster, onto the boat, where they feast on milk and bread. That night, the boat unmoors itself, leaving the children adrift at sea with little hope that Father Grijpma might find them. The next day, a fishing captain from the coastal area of Urk boards the houseboat looking for survivors and, finding the children, gruffly orders them and their pets aboard his boat. Although they fear that the Captain is a pirate, the ship's cook fixes them a hot meal and gently tucks the children into bed. After the Captain finds the last of the survivors in the area, he orders the ship to move to search elsewhere, causing the children to assume that they will never see Father Grijpma again. The next day, softened by the children's fear, the Captain tells them a story about another flood in which survivors' hearts were lightened after seeing a cat save a baby by keeping its cradle afloat. He then leads the children in a fantastical song. Days later, after rescuing a dozen more grateful survivors, the Captain decides to return to Amsterdam for food and medical attention, assuring the children that the hospital boats will have lists of missing persons to aid them in finding Father Grijpma. That night the Captain tells the children a fairy tale: Sailor Jan promises his lover that upon returning from his next voyage, they will be married. When his boat is later reported missing, the lover waits patiently for a year believing that Jan will come home. After she asks many returning sailors for news of Jan's ship, one mysterious captain offers to take her to him, but only if she will give him her soul. After she agrees, the captain turns her into a mermaid. Swimming through sunken ships and villages searching for her Jan, the mermaid finally meets an old wise man and learns that in trade for her soul Jan has finally been able to return home. Trapped in the sea forever, the mermaid spends her time singing warnings to sailors of oncoming storms. The morning after the Captain finishes his story, his boat arrives at the Amsterdam port, where naval officers reprimand the Captain for not following protocol. After the Captain rudely rebuffs them, he explains to the children that the frustrated Navy can only bark out orders to other ships, because its own ships displace too much water to enter the flooded areas and save people. Meanwhile, the children want to remain onboard and make the Captain their new father, but he insists that they go to a hospital ship. Boarded with the radio operator Sparks, Adinda and Jan are forlorn over the loss of the Captain, but Miss Winter, a nurse, comforts them with imaginary spells. Late that night, Jan overhears the adults' plans to send Jan and Adinda to an orphanage and send a rescue ship to Niewerland, manned by Captain Tandema. The next day, the children stow away with their pets in empty coffins being loaded onto the rescue ship. Soon after the ship embarks, Bussy's howls and Prince's crowing alert Sparks and Miss Winter that the children are aboard, but the ship must continue on its course to Niewerland. After hearing in the village that Father Grijpma left on a fishing boat the previous night, the children then see the Captain, who tells Tandema that he feels responsible for the children and will take them with him. Hearing that a grief-crazed farmer and his son are trapped in their barn attic, the Captain offers to rescue them. The Captain and Cook row to the barn with Adinda and Jan, whose kind words convince the boy and his father to join them. When the mute and fearful farmer refuses to leave the row boat, Cook stays with him as the Captain tows the boat behind his into a harbor. Once there, photographers, greedy for a story about the "crazy" farmer, blind him with their flashbulbs. In a state of shock, the farmer stabs the Cook with his pitchfork, killing him. Sobered by the tragedy and the arrival of "professionals," the Captain decides to retire from the rescue mission and return to the children's village in the hope of finding their father. Arriving at the village, the children hear their father's organ and rush to the dilapidated church, where Father Grijpma gladly embraces them. As a group of singing children march by to school, the Captain bids farewell, promising to return and visit Adinda and Jan.