Amy Alden recovers from a car accident, waking up to find that her mother has died and her father, Thomas, is there to take her to Canada. When Amy arrives in Canada she learns that her estranged father is an eccentric sculptor, inventor and ultra-light aircraft pioneer. Thomas' character is based on Canadian inventor and sculpture Bill Lishman and his work with naturalist Bill Carrick. The opening scene symbolises the journey of the geese Amy adopts.
Thomas wakes up to the sound of tractors destroying the neighbouring marsh. Amy refuses to go to school, seeking solace in the marsh instead - a motif for her own life. While exploring the damaged environment, Amy finds a nest of abandoned goose eggs. Deciding to care for them, Amy turns a chest of drawers into a makeshift incubator. The next evening, while her father is at a town meeting, Amy finds that the goslings have begun to hatch.
Amy's sense of place and happiness improve as she cares for the geese. Amy tells Thomas the feeding schedule and asks if he can handle the responsibility, teasing his lack of parental skills. Thomas seeks advice from game warden Glen, who tells the family that domestic geese don't learn to migrate and have to be pinioned (clipped). Amy protests and Thomas kicks Glen off his property. Amy freaks out after a mishap in the shower, and Susan reassures her they will protect the geese to calm her.
Thomas and his brother, David, consider the flight speed of geese and test a new engine on Thomas' ultra-light craft. Back in the barn, Amy teaches the geese to chase her, and starts to bond with Uncle David. That evening, Thomas suggests they work together to prepare the geese for flight. David and Thomas' characters are based on the work of Bill Lishman and Bill Carrick, co-founders of Operation Migration, a not for profit that sought to teach captive-raised birds to migrate.
Although training goes well, the natural instincts of 'imprinting' means the geese remain attached to Amy. Thomas worries he has let her down again. While Thomas and Susan talk, Amy sneaks into the ultra-light. Amy proves the geese will fly behind her, but also has a minor crash. Thomas finds Amy unharmed but is shaken by the idea of loosing her again. Later, Thomas suggests building a custom aircraft for Amy, selling off old sculptures to pay for it.
Thomas teaches Amy to fly her ultra-light. The next day, Amy is given a chance to try flying alone. During her flight, the geese escape from their coop and join. Igor, with the limp, remains flightless. That evening, Glen, the game warden, visits the property to intimidate Amy and Thomas. Uncle David visits a naturalist (based on William JL Sladen) to discuss sanctuaries, the possibility of light aircraft assisting migration for rare birds and the future of a North Carolina marshland.
The family begin preparing for the migration south and training the geese. Igor, with a little extra encouragement, manages flight but gets into an accident and goes down in the forest. While looking for Igor, Glen the game warden steals the rest of the flock. Amy, Thomas, Barry and David plot an elaborate escape for the birds, and begin their migration early.
The flock joins a population of migrating wild geese, separating from Amy and Thomas. Thomas and Amy follow the birds, deterring the poachers and making an unscheduled landing. That night, Amy asks Thomas why he never visited her, pressing him for an honest answer. The next day Thomas ultra-light suffers structural failure. Thomas tells Amy she must continue the journey alone, but Amy is hesitant. Thomas reassures her that she is strong and capable, just like her mother.
Amy makes the last leg of the journey alone. Meanwhile, at the North Carolina sanctuary, a crowd of environmentalists protest the imminent destruction of the marshes. Knowing Amy is due to arrive that day, naturalist Dr Killan blocks a bulldozer. The crowd cheers as Amy and the flock arrive, effectively teaching the birds to migrate and saving the habitat from development. The journey of the geese also symbolises Amy's journey through loss, migration, accepting her new family.
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