The movie begins with a short Patchy the Pirate segment. Patchy tells the audience that they will be watching his favorite episode, "Weekenders Are Flying Away Home," but Potty shoots him out of a cannon.
After her mother dies in a car accident, 13-year-old Amy Alden (Anna Paquin) is brought from New Zealand to Ontario, Canada, by her estranged father Thomas Alden (Jeff Daniels), a sculptor and inventor, to live with him and his girlfriend Susan (Dana Delany).
When a construction crew destroys a small wilderness area near the Alden home, Amy finds a nest of goose eggs. Without Thomas, Susan, or her uncle David (Terry Kinney) knowing, she takes the eggs and keeps them in a dresser in her father’s old barn to incubate. When the eggs have hatched, she is allowed to keep the goslings as pets. Thomas asks for help from local game warden Glen Seifert (Jeremy Ratchford) on how to care for the geese. Seifert comes over to the Alden house, and explains that the geese have imprinted on Amy as their mother. He explains that geese learn everything from their parents including migratory routes, but also warns Thomas that all domestic geese must have their wings pinioned (clipped) to render them flightless, which upsets Amy. Thomas throws Seifert off his property, only for Seifert to threaten the Aldens that if the birds start flying, he will have to confiscate them.
Thomas decides to use an ultralight aircraft to teach the birds to fly and show them their migratory routes, but quickly realizes the birds will only follow Amy. Aided by his friend Barry (Holter Graham), Thomas teaches Amy how to fly an ultralight aircraft of her own, so she can teach the geese. David mentions knowing someone running a bird sanctuary in North Carolina, and arranges for the geese to go to the sanctuary. The birds have to arrive before November 1, or the sanctuary will be torn down by developers who plan to turn it into a coastal housing development.
Amy and Thomas practice flying the aircraft, but Igor, the weakest of the geese, who has a limp, accidentally hits the front of Amy’s aircraft and lands in an isolated forest. While the group goes off to search for the bird, Glen Seifert returns to the Alden farm and confiscates the other geese. The next day, an elaborate plan is staged to free the geese and start their migration to North Carolina.
Making an emergency landing at Niagara Falls Air Reserve Station in upstate New York on the south shore of Lake Ontario, Amy and Thomas almost get arrested. They become national news, with residents cheering them on and offering the two a place to stay at night at each of their stops. Thirty miles before reaching the bird sanctuary, Thomas’s aircraft suffers a structural failure and crashes in a cornfield; he tells Amy to finish the journey by herself. After Amy takes off and begins to head toward the sanctuary, Thomas hitchhikes to the bird sanctuary. While waiting for the geese, Thomas, Susan, David, Barry and many animal enthusiasts stand up to 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. The following spring, all 16 geese safely return to the Aldens' farm on their own.
The movie itself ends and Patchy returns to greet the audience. After a totally random outburst in which he tells the audience to walk the plank, he announces that they are going to read a fan letter. Unfortunately, Potty shows up with a fuse in his head from an evidently unplanned explosives stunt. Potty and Patchy are blown up and Patchy decides to sign off the show.