In 1962 a seal drowns in a fishing net cast by the film's main antagonist, the financially struggling fisherman, Billy Baker (Keith Szarabajka) - much to his fury. He and the other local fishermen discuss shooting the seals as a way to improve their flagging fishing season. Toni Whitney (Tina Majorino), a seven-year-old girl, and her Rockport, Maine family subsequently adopt the seal's orphaned newborn pup (played by a sea lion named Tory), naming it Andre. The vet doesn't hold out much hope, but Toni incites him to survive, with the promise that she will be his best friend forever, and that she will always take care of him. After several failed attempts to get him to take a bottle - with both warm and cold milk - Toni's father, Harry (Keith Carradine), the harbor master, constructs an "artificial mother" for him out of wetsuit material, a bucket, and two feeding bottles, which he finally accepts, ensuring his survival.
As Andre grows up, Toni forms an inseparable bond with him, even taking him to school for show and tell, with the help of Harry and the permission of her teacher, the prim and prickly Mrs. McCann (Shirley Broderick). He becomes attached to the Whitneys - especially to Toni - living in the harbor, learning tricks, and attracting a huge local following of fans. The irony of his success as an entertainer further angers Billy, who becomes increasingly jealous of Andre's and the Whitneys' success and esteem within the village. Relations between Harry and Billy deteriorate rapidly. Meanwhile, Billy's son, Mark (Joshua Jackson), and Toni's sister, Paula (Aidan Pendleton), become romantically involved, increasing tension between Paula and Harry over Andre. Mark and Billy have a strained relationship as it is. Under pressure from his family and the locals, Harry reluctantly makes the decision to release Andre into the wild once he is weaned, but reconsiders and does not go through with it when he encounters the body of a seal covered in bullet holes at the place where he had planned to release him.
In his first winter, Andre escapes the confines of the barn, and the water home that Harry built for him there when the harbor froze over. He cuts himself badly - leaving a trail of blood which the Whitneys discover upon realizing that he is missing - and remains gone for the winter. However he returns in spring, physically weak but unchanged in character, and recovers quickly from his ordeal.
As Andre gets older he continues to be scapegoat for the local fishermen - and for Paula - as he takes up more and more of Harry's time and affections. He misses her performance (which he told her he would not miss for the world) in the local Miss Liberty beauty pageant, because he has to protect Andre from a drunken Billy, who is trying to kill him with a pitchfork. Harry's relations with his son, Steve (Shane Meier), fade into the background as he comes down harshly on him for minor transgressions, and fails to keep up with what is going on in his life. When Paula and Mark are discovered smoking in the shed when Andre exits it in a fit of coughing, Harry permanently bans Mark's presence on the Whitneys' grounds, and his and Paula's relationship - in part a displacement of the tension between Harry and Billy. Paula decides she is leaving home, raging that Harry doesn't care about her, and that she hates him - to the anger and deep concern of her mother, Thalice (Chelsea Field). Mark tells her he knows a way to make Andre go away so that he'll never come back.
Harry's job also suffers. He fails to call meetings, never checks moorings, and his relations with the fishermen become ever more strained. He also attracts the ongoing attention of the federal government, who send their inspector, Jack Adams, to inform him that he is flouting the law by keeping a wild animal in captivity, as a pet. He insists that Andre is there by his own choice, but that it's too dangerous in the wild during winter. Jack pays two visits to the Whitneys' home, increasingly emphatic that Harry faces court and even jail if he does not give Andre up. However, Andre is teaching him about the intelligence and abilities of seals, and despite the risks, he is determined that nothing will put an end to this learning curve. At one point Andre saves his life when he is underwater checking a mooring - which turns out to be entangled in an active explosive.
Eventually, Thalice manages to impress upon Harry the high cost of continuing his relations with Andre in the setup that they have, and he agrees to call Jack, so that he can relocate Andre to the aquarium in Boston, where he will be safe, cared for, and have plenty of people for company. However, before he can tell Toni, the telephone rings, and she goes down to the harbor. There she discovers that Paula and Mark have taken Andre, commandeered a boat, and are heading out to sea as dark clouds gather. Steve is charged with keeping an eye on Toni while their parents investigate, but he is engrossed in a TV program, and does not notice her slip out and launch the dinghy onto an increasingly choppy sea.
In Mark and Paula's boat, he attempts to shoot Andre, reasoning that he is a problem for the fishermen, but she finally realizes that she does care about Andre and doesn't want him to be hurt or killed. She tries to stop Mark from shooting, but the gun goes off. Andre jumps overboard, but Paula, not seeing this, assumes his body has fallen in. Very upset, and very angry at Mark, she demands to be taken home. Harry and Thalice, having been informed by Toni that Paula and Mark had taken Andre, meet them on the shore, whereupon Steve, in a panic, arrives and tells Thalice that Toni has disappeared, as has the dinghy. She calls the coast guard, as the rain starts to fall, and visibility begins to deteriorate.
Out at sea, Toni is struggling to maintain control of the dinghy in the face of the storm and a strong outward tide-rush. It's being tossed on huge waves, in opaque rain, and is heading towards some jagged rocks. She loses both oars, and, panicking, begins to call for help. Andre, who turns out to be unharmed, swims to her rescue, pulling her away from the rocks by the dinghy's mooring rope. He then alerts Billy and Harry, in their boat, leading them to Toni's location. Before she can be rescued, a large wave capsizes the dinghy. Mark, who came with Billy and Harry, jumps overboard, swims out to her, and Billy throws them both a lifebelt, pulling them to safety. Billy tells Mark that he is proud of him, while Harry comforts Toni in the back of the boat, and Andre swims away, exultant at her safety.
Once back on shore, Toni is distraught to find Jack levering a caged Andre onto a transport vehicle. Harry explains to her that Andre is going to live in the aquarium in Boston, where he will be safe and cared for in ways they can't. Annie Potts, an aquarium worker, tells Toni they will take good care of him, that they will love having him there, and that she will get to visit him whenever she wants. She reluctantly accepts the notion, and tells Andre that she loves him and will visit him all the time.
As summer comes round, Billy and Mark's relationship improves. Harry repairs relations with his family, and having been offered a research job in marine mammal protection, steps down as harbor master, nominating Billy to take his place. Toni comes to the realization that Andre would be happier in the wild, being a wild animal, and he is subsequently released. The Whitneys do not expect to see him again - Toni wonders if he is making new friends with the wild seals, and Paula professes to miss him. Multiple alleged sightings of Andre are reported, until a friend of the Whitneys spots him nearby, and informs them that he is on his way. The entire town of Rockport flocks to the harbor to watch him returning home to his family. The film ends with an adult Toni narrating that his life became legend after he made his first trip home - that he spent every winter at the aquarium, and every spring he was released to swim home to Rockport, where he spent his summers. She narrates that by the time he was twenty-four years old he could hardly see, but still made his final trip home, and that in all her past and future, she'll never have a better friend than him.
- Keith Carradine as Harry Whitney
- Chelsea Field as Thalice Whitney
- Tina Majorino as Toni Whitney
- Aidan Pendleton as Paula Whitney
- Shane Meier as Steve Whitney
- Keith Szarabajka as Billy Baker
- Joshua Jackson as Mark Baker
- Shirley Broderick as Mrs. McCann
- Andrea Libman as Mary May
- Joy Coghill as Betsy
- Gregory Edward Smith as Bobbye
- Tory as Andre, based on the real seal Andre the Seal