Amy Alden (played by Anna Paquin) was born in the summer of 1982 to Thomas and Aliane Alden in Southeastern Ontario, Canada. Her father was an eccentric sculptor and inventor and her mother, a recording artist. She lived the three first years of her life on the family farm in Ontario before her parents' separation. Her mother then took her to New Zealand where her father seldom came to visit and she somehow resented him for this.
On a rainy night when Amy was thirteen, she and her mother took a drive and a truck hit them full speed while a distracted Aliane spoke on her cellular phone. The vehicle crashed and the mother died, but Amy survived. Thomas Alden flew to New Zealand for the funeral and took Amy back with him to Canada in the spring of 1995. Amy didn't remember the early years in Ontario and her father had become a stranger to her. It was a difficult adaptation and the atmosphere was tense. Amy was not pleased to discover her father had met another woman named Susan Barnes who often came to the farm and helped him with his work.
One day, Amy skipped school and began exploring around the farm where an urban development team had uprooted trees and destroyed some nesting Canada geese's habitat. Amy noticed sixteen abandoned goose eggs among the debris and took them to the barn where she hid them away in a makeshift incubator built into a drawer. She kept her discovery a secret, and the following night, she sneaked out to the barn to find the goslings had hatched. She was the first living thing the birds saw and they imprinted on her. Her father allowed her to keep them, but wondered how they should take care of them. He went to the local Animal Regulation Authority office where he spoke to officer Glen Seifert who told him how to feed them and offered to come over on the week-end. Meanwhile, Amy enjoyed running around the farm with the goslings following her everywhere. When officer Seifert finally came, he explained that the Aldens would only be allowed to keep the geese if their wings were clipped; without parental influence, they would constantly land on private properties and be a nuisance to the community. Amy flew into a rage when he attempted to clip one of the goslings' wings with a nail clipper. She hit him with a pop corn bowl, gathered the geese in it and locked herself up in the bathroom. She believed her father had done this on purpose, but the following morning, Susan had an honest conversation with her, explained what had really happened and offered her friendship, asking Amy's trust in return. Amy broke down and began to cry, allowing Susan to embrace her.
Summer came and the geese grew. Amy's father was fascinated to see how the birds followed her so closely, even when she rode a four-wheeler. It occured to him that the geese might follow an airplane and be able to migrate this way. Thomas, who flew gliders, began experimenting with motorized prototypes aided by his friend Barry Strickland and his brother David who had moved to the farm to help Thomas catch up with his work. Amy thought this was a crazy idea, but her father convinced her to try. Amy collaborated with her father, teaching the geese to trust him and follow him as well so that when fall came, they would agree to follow his ultralight aircraft and head South. This was successful on the ground, but not so much with the aircraft. On a whim, Amy decided to try using the aircraft herself while her father wasn't looking. She nearly broke her neck, but the geese did follow. Thomas decided to get Amy an aircraft of her own and teach her to fly so that they could both lead the geese South. Amy was overjoyed, but Susan thought it was irresponsible. When the first experiments proved successful, the Aldens began to determine a migration route. David Alden proposed to take a trip to North Carolina to visit Doctor Killian, an ornithologist of his acquaintance. Doctor Killian informed him about a local wetland developers meant to destroy and build upon; if migratory birds were to show up by November first to winter in the area, the wetland would be protected by law. The location was ideal, and all agreed on it.
After much preparation and training the geese to fly for long periods of time, the Aldens went on an excursion with the aircrafts and a goose named Igor got hit by Amy's ultralight and fell into the forest. Amy was frantic. The team went to look for the bird and finally found him alive but missing primary feathers preventing him from taking part in the migration. Amy picked him up and brought him to the barn to discover all the other geese had been confiscated by the Animal Regulation Authority while they were away. The following day, Igor was tied behind Amy in her aircraft and the Aldens took off, flying close to the Animal Regulation office where Barry and David had managed to find and release the caged animals. The flock flew up hearing Amy's voice on Barry's radio and engaged their journey to North Carolina.
The flight over Lake Ontario was very long and the Aldens had to make an emergency landing at Niagara Air Force Base in New York state. This caused much commotion and Amy's story appeared in the media. This attracted the attention of tree huggers who gathered at the North Carolina wetland with Doctor Killian to denounce the developers' project and welcome Amy and the geese. On their way to the wetland, Thomas had an aircraft malfunction and fell into a corn field. Amy landed in panic and ran to her father who had hurt his arm. Amy was reluctant to continue on her own and felt that she couldn't leave her father there nor find her way without him, but he assured her that she could. After some indications, Amy took off and headed for the wetland on her own, pondering on everything that had happened in the recent months. A crowd of supporters cheered at her arrival and she embraced her uncle David, Susan and Barry who were waiting for her as well as her father who had hitchhiked his way to the site.
In the following spring, Amy's adopted geese flew back to the Ontario farm on their own, including Igor.
The character of Amy Alden is not based on an actual individual as is the case with Thomas Alden who is directly inspired from Canadian inventor Bill Lishman, but Lishman has a daughter, Carmen Lishman, who took part in her father's work with Operation Migration. Carmen was Amy Alden's age when Fly Away Home was made and appears in the film as one of Amy's classmates.
Many elements of Amy's life mirror actress Anna Paquin's life, such as a Canadian birth and an early move to New Zealand, divorced parents and musical talent (Amy plays tuba, Anna Paquin plays cello). The Fly Away Home actors were granted a lot of latitude in the elaboration of their characters and the action taking place in the various scenes. The nose ring, a sign of Amy Alden growing up and reaching her teenage years, was Paquin's own idea and request.