The initial scenes of the movie show a school of dolphins in their natural state, followed by a crab fisherman returning a crab trap to the ocean after emptying the trap of its contents. Sawyer Nelson (Nathan Gamble) is biking along the beach when a fisherman calls for help after finding an injured bottlenose dolphin tangled in a crab trap. The two call for assistance, and rescue workers from the Clearwater Marine Hospital, run by Dr. Clay Haskett (Harry Connick Jr.), take the injured dolphin for treatment. Clay's daughter Hazel (Cozi Zuehlsdorff) names the dolphin Winter, as two prior dolphins (Summer and Autumn) were successfully returned to the ocean, and believes that using seasons as names will continue the streak. She allows Sawyer to see Winter; Clay initially does not like the arrangement since Sawyer is not trained in marine animal care; however, after noticing that Winter responds well whenever Sawyer is around, he is allowed to visit. Afterwards Sawyer (who was enrolled in summer school due to him failing or nearly failing all his classes during the year) skips classes to daily visit Winter.
Unfortunately, Winter's tail is irreparably damaged and thus must be amputated. Sawyer's mother Lorraine (Ashley Judd) finds out about Sawyer skipping classes, but after seeing that Sawyer's interaction with Winter has improved his moods and well-being (something Sawyer had not shown since being abandoned by his father who disappeared while going on a visit five years earlier), she withdraws him from summer school and allows him to volunteer at the hospital. Winter learns to swim without a tail by developing a side-to-side motion (like a fish), but after an x-ray Dr. Haskett notices that the unnatural motion is causing stress on her spine; if continued the motion will eventually kill her.
Meanwhile, Sawyer's cousin Kyle, a champion swimmer, returns from the military with a damaged right leg from an explosion (later requiring amputation). Sawyer visits him at the local Department of Veterans Affairs Medical Center, where he meets Dr. Cameron McCarthy (played by Morgan Freeman) who specializes in prosthetics. Sawyer thinks that a prosthetic tail may be the solution for Winter's future health and asks Dr. McCarthy to assist; he agrees to work on the project during his upcoming vacation, and convinces his prosthetic supplier (Hanger Prosthetics and Orthotics, who supplies Winter's real-life tails) to supply the parts at no cost. Dr. McCarthy manufactures a "homemade" model tail while waiting for the real one to arrive; however, Winter destroys it by banging it in the pool
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Shortly thereafter the hospital (already in financial straits) is seriously damaged by "Hurricane LeRoy", whereupon the board of directors agree to close the hospital, sell the land to a real estate developer, and find homes for the other residents (except Winter, who due to her condition is not relocatable and may have to be euthanized). However, after a chance encounter with a mother and daughter (who heard about Winter's story and drove all the way from Atlanta to see her; the daughter is also missing a left leg), Sawyer comes up with a last-chance plan, "Save Winter Day", to save the facility. Dr. Haskett is not sold on the idea, but reconsiders after talking with his father, Reed (Kris Kristofferson). Kyle agrees to a race against Donovan (who followed him at high school and broke nearly all his prior swim records) and enlists a female friend at Bay News 9 to promote the event.
The Hanger-supplied tail finally arrives; however, Winter damages it as well. Sawyer discovers that Winter isn't rejecting the tail; instead, the sock to which the tail is attached is irritating her skin. Dr. McCarthy comes up with an alternative gel-like sock (which he calls "WintersGel", the real-life name of the Hanger product used to attach prosthetic limbs, which was developed during its research with Winter); and finally on Save Winter Day she is able to accept the new sock and tail. At Save Winter Day, Sawyer's teacher gives him credit for his work at the hospital; thus, Sawyer has passed summer school despite not attending formal classes. The fisherman who initially spotted Winter places $40 in the donation jar (saying "we have a history together"). The board learned that the real estate deal closed (thus selling the facility); however, the developer (who attended the event with his grandchildren) agrees to allow the hospital to remain open.
The ending shows scenes from Winter's actual rescue in December 2005, several of the prosthetic tails that Winter has worn, and scenes from real amputees who have visited Winter at the Clearwater Marine Aquarium.
