In New Zealand, 13-year-old Amy Alden (Anna Paquin) is involved in a car accident with her mother, which results in her mother’s death. Amy is taken back to her new home in Ontario by her inventor father Thomas Alden (Jeff Daniels), who later introduces her to his girlfriend, Susan (Dana Delany). While Amy is initially hostile towards her dad and Susan, she eventually grows fond of both.
After a construction crew destroys a small wilderness area of birds in the Alden family’s backyard, Amy decides to check out the scene only to find a bunch of eggs left behind by their parents. Without Thomas, Susan or her uncle David (Terry Kinney) knowing, she takes the eggs and sticks them in a dresser located in her father’s old barn to incubate them. When she comes back from school, she discovers that the eggs have hatched and Thomas allows her to keep the birds.
After asking for help from a local game warden (Jeremy Ratchford) on how to help care for the geese, the warden comes over to the Alden house where he says all domestic geese must have their wings pinioned (clipped) in order to render them flightless. When the game warden attempts this on one of the geese, it upsets Amy. Thomas throws the game warden off his property where the warden threatens that if the birds start flying, he will have to confiscate them.
Thomas begins doing research and learns that if the birds aren’t taught to fly properly, they will fly off on their own and get lost or possibly not survive the winter. He enacts a plan to use a homemade aircraft to teach the birds to fly. When the birds fail to follow him, he comes up with the following plan: teach Amy to fly and the birds will follow her because they already do the same thing on land due to Amy being imprinted as their mother. Susan is disgusted at hearing the news as, the previous day, Amy had hopped in one of Thomas’s aircraft and almost killed herself when the aircraft crashed.
Thomas (Jeff Daniels) attempts to get the geese to follow him.
Thomas, Susan, David and Thomas’s friend Barry (Holter Graham) attempt to teach the birds to fly, with success. David travels down to North Carolina to talk to a friend who owns a bird sanctuary about the plan, who initially finds the plan both ludicrous and impossible but also mentions that if no birds reach the sanctuary by November 1, it will be torn down by developers who plan to turn it into a housing development.
Amy and Thomas practice flying the aircraft, but Igor (the weakest and slowest goose of the bunch) accidentally hits the wing of Amy’s aircraft, both injuring the bird and denting the aircraft’s wing, and lands in a forest. While the gang goes off to search for the bird, the game warden, keeping his promise to confiscate the birds and who witnessed the Aldens practicing for the big flight, comes to the Alden barn and seizes the geese. The next day, after having found Igor and getting back the geese, the gang sets off on their quest to migrate the geese.
After making an emergency landing at a U.S. Air Force base on Lake Ontario and almost getting arrested, Amy and Thomas become national news with the U.S. cheering them on and residents giving the Aldens a place to stay at night at each of their stops. Thirty miles before reaching the bird sanctuary, Thomas’s aircraft crashes in a grassy field and he commands Amy to finish the journey by herself. After Amy takes off and begins to head toward the sanctuary, Thomas hitchhikes a ride with a local group of hippies who take him to the bird sanctuary. While waiting for Amy, Thomas, Susan, Barry and many hippies, tree huggers, townspeople and animal enthusiasts stand up to the large crowd of developers who are waiting to start the excavation of the site. Amy eventually appears with the geese, much to the joy of the townspeople and Amy’s family, but to the dismay of the developers. The townspeople and the Aldens celebrate their victory.
Before the credits roll, it is revealed that all 16 geese, including Igor, returned to the Alden’s farm the next spring safely and all on their own.