Thirteen year-old Amy (Anna Paquin
) is riding passenger with her mother (Deborah Verginella
) in their car one rainy night in New Zealand. All seems right and pleasant until the mother loses control of the car and crashes. Amy awakens later in the hospital to find her father, Thomas Alden (Jeff Daniels
), who says that he's come to take her home with him to Canada. Her mother has perished in the accident. Thomas brings her back home to his farm where he's evidently been used to living on his own for a while; most of the rooms in the house are used to store works of art and the barn has become his workshop. Amy isnt used to the transition and claims she doesn't remember anything about living there. Her displeasure is further fueled when her father introduces her to his girlfriend, Susan (Dana Delany
). Amy responds to the introduction with quiet hostility.
As Amy tries to become adjusted to her new life, she finds her father's traits difficult to accept at first. One morning he angrily runs out of the house clad in nothing but his underwear to confront a construction team deforesting the area around his home. Another day, Amy finds him testing a new invention for flight; an aluminum glider strapped to his shoulders which he soon crashes in the surrounding field. Scared and unsure if her father's all right after the crash, Amy shuts herself in the house when he finally emerges and shouts triumphantly.
One day, while exploring the area around the Alden farm, Amy comes across a portion destroyed by the construction crews. Under a fallen tree, she discovers an abandoned nest of goose eggs, some of which emit weak chirps. She gathers all the eggs and brings them back to the barn where an old bureau stuffed with scarves and cloth provides a safe place to put them. She takes a heating lamp from her father's workshop and uses it to provide light and warmth for the eggs. The next morning, as she's preparing for her first day at school, she stumbles on her uncle David (Terry Kinney
) who Thomas invited over to help with his work. She's quickly ushered out the door and impatiently sits through her classes as the first of the eggs begin to hatch. When she arrives home, she greets her father and Susan who say theyre going to a town meeting. Amy later takes advantage of her uncle's distracted attention and sneaks away to the barn where she finds the newly hatched goslings. They look at each other and a bond immediately forms.
At the meeting, Thomas speaks out against the construction thats been destroying the habitats around his home but is criticized by one of the drivers who says he's merely performing a job to provide income for his family. The local game warden (Jeremy Ratchford
) draws attention when he addresses the threat of construction not only towards local home owners, but to the wildlife. Thomas and Susan return home to find Amy missing and frantically search for her in the night fog with a remorseful David. However, they find her sleeping in the barn surrounded by her hatchlings. When she wakes up, she asks if she can keep them.
Though Thomas is welcome to do anything for his daughter's happiness, hes less than enthused about sharing space with a flock of geese. He goes to the game warden, Glen, and issues his concerns. Glen gives general advice and stops by the farm to observe the goslings following Amy around the property, a trait called imprinting where baby geese or ducks assume the first thing it sees is its mother and will follow. At the house, he attempts to pinion the geese in accordance to a law that states all domestic geese must be rendered flightless. It would involve cutting off the first wing joint of each of the goslings, something Amy objects to by hitting Glen over the head with her popcorn bowl. She quickly gathers up her geese in the bowl and locks herself in the bathroom while Thomas forcefully ejects Glen from the house. Glen threatens that he will have to confiscate the geese if they start flying. Thomas tries to apologize to Amy but she refuses to come out. She spends the night in the bathroom.
The next morning, Thomas' friend Barry (Holter Graham
) stops by the farm to visit while Amy is in the shower with her goslings. When she accidentally sprays soap into her eyes and steps out of the shower screaming, chaos ensues after Thomas breaks the bathroom door in to expose the naked Amy. Susan shoves a shaken Thomas out of the bathroom and tries to console Amy. Amy lets out her frustrations of having to live with her father who is 'so weird' and her anger towards the game warden. Susan says that she knows she cannot replace Amy's mother, but that she can be her friend and assures her, as a friend, that nothing will happen to the geese.
Thomas realizes that the realities of the geese flying is a real problem and devises a way to show the birds how to migrate south. With the help of David and Barry he upgrades his glider with a series of engines to maintain flight until he is able to construct a frame that he can sit in and control the plane with. He introduces the idea of leading the birds south to Amy, who is hesitant but agrees to help. Still, no matter how many times they try, the geese prefer to stick close to Amy rather than follow Thomas in his plane. Frustrated, Amy decides to try manning the plane herself and manages to get airborne, with the geese following, before crashing into a fence. Thomas finds her alive and well but breaks down, having thought the worst.
Despite that, having seen the slight success of Amy's ill-fated flight test, Thomas proposes to Susan that he teach Amy to fly a new glider and lead her and the geese south. Susan thinks the idea is ludicrous but Amy is excited. Thomas sells one of his art pieces, a model of the lunar lander, to fund construction of a new glider complete with goose wings and head. He teaches Amy how to pilot it and, to everyone's elation, the geese follow her in flight. David is able to contact a bird enthusiast and entrepreneur, Dr. Killian (David Hemblen
) about introducing the geese to a local bird sanctuary in South Carolina. The expert explains that if the geese are able to land by a certain date, the land is theirs.
Meanwhile, Thomas and Amy continue training the geese in flight, making them stronger and discussing flight paths and when their takeoff date should be. However, on one training flight, Igor, a goose born with a limp and hesitant to fly, is accidentally knocked out of the air when he flies into Amy's plane. Fortunately, he is found later by Amy and the others during a night search in the woods. During this time, however, Glen revisits the farm and confiscates all the geese in their crates unnoticed.
The next day, Thomas picks up Amy during lunch period from school while David drives down to the game warden's office claiming to have hit a mysterious creature during the night. Glen is teaching school children about conservation while all this is happening. As David takes the officer at reception to his, now empty, truck and suggests scanning the area for the missing beast, Sharon and Barry spring the geese loose from the back of the building and herd them into flight as Thomas and Amy pass overhead in their planes, beginning the flight south. As they pass over the school, Glen is left speechless.
After crossing Lake Ontario, low fuel forces Thomas and Amy to land on an army base where they are quickly taken into custody. After they tell their story, however, they are welcomed and allowed to stay the night before leaving the following morning with plenty of news reporters documenting their amazing journey. At one point Amy's geese become distracted by a large flock of wild geese and follow them into marshlands where hunters take aim at them. Amy and Thomas fly in low, shocking the hunters, and land to search for the geese. They come across an old woman with a shotgun (Gladys O'Connor
) who offers them residence when she discovers that Amy is 'the little girl I saw on television'. Back en route, Amy and Thomas find themselves in thick fog and descend into a dense city, narrowly missing skyscrapers while navigating the main street below.
On the last day of their trip, Susan, David, and Barry arrive at the bird sanctuary early to find a crowd of people waiting for Amy and the geese, shouting their support and protesting against a corporation bent on bulldozing the sanctuary. As Amy and Thomas get nearer, Thomas' plane malfunctions and he crashes into a field. He persuades Amy to fly ahead, saying that she's got her mothers spirit and that she will make it to the sanctuary. Thomas rides ahead and makes it to the sanctuary in time to see Amy fly in over the dunes and land safely to cheers of hundreds, both on site and watching on TV. Reporters flock to her as her geese flock happily to their new winter home.
An epilogue video shows Amy waking up on an early spring morning to the sounds of her geese returning along the route she had led them on, testing their feet on a still frozen pond.