Grace eventually recovers physically, though she is left with a partial leg amputation and remains listless and psychologically scarred and prone to anger. However, her horse is traumatized and uncontrollable to the extent that it is suggested he be put down. Grace's mother, Annie (Kristin Scott Thomas), a brilliant editor, is horrified, since she knows this will involve shooting Pilgrim and she refuses to have Pilgrim destroyed that way.
Meanwhile, Annie and her husband, Robert (Sam Neill) have serious marital problems of their own. Robert is rather self-centered, emotionally unsupportive of Annie in general, and he disparages Annie's desire to help Pilgrim survive and recover. Annie has grown apart from Robert in the past few years and neither are sure they love each other anymore.
Knowing that it is up to her to heal both her daughter and her daughter's horse, Annie contacts Tom Booker (Redford), a "Horse Whisperer", who agrees to help, on the condition that the despondent Grace takes part in the process. Since Tom is reluctant to fly from Montana to New York, Annie must pack a struggling Pilgrim and a moody, combative Grace into her own car and trailer and drive thousands of miles westward to the Booker ranch.
It's also a matter of two subcultures meeting when a determined, sophisticated, uptight Annie talks a laid-back, relaxed, calm Tom into helping heal Pilgrim. Annie is fearful of the unfamiliar open spaces of ranch life and the dark, dark nights without signs, restaurants, stores, or good lighting. She is also apprehensive about this alien, strange culture that she and her daughter have entered. However, as with most of her many fears and insecurity, Annie masks it behind a know-it-all bravado, which Grace calls her on.
As for the small-town Booker family, they are curious about Annie and Grace. Diane wonders out loud where on earth Annie is from since Annie's accent sounds so foreign and strange to her; never have the Bookers met someone as exotic as Annie nor are they at all familiar with the sophisticated, intellectual, streetwise city world that she and Grace live in.
But since Tom briefly lived in Chicago, he somewhat understands Annie's city world and her sophistication; he also is the first to sense that lurking underneath her steely bravado, controlled exterior, and grittiness are many deep fears and a low self-esteem.
As Tom and Grace work with Pilgrim, it becomes clear that Annie also has unhealed psychological wounds to deal with; the country life makes that glaringly clear when Annie comes to realize that she cannot run from her fears and issues forever and must begin to face them down instead of hiding from them behind a know-it-all coat of armor. She also realizes that she has been afraid to pursue her true dream she's carried since her childhood...to become an author.
Matters are complicated more when Annie begins to fall in love with Tom, which forces her to realize that she must do something about her dysfunctional marriage to Robert, another issue she has been afraid to confront.
Pilgrim and Grace slowly heal and overcome their trauma while Annie and Tom are faced with a potentially sticky situation when they are attracted to each other and Robert shows up on the ranch unexpectedly.
Robert suspects Tom is attracted to Annie and although he is cordial with Tom, inside he is fuming and privately makes some rather cruel remarks to Annie questioning whether she ever really loved him.
Annie and Tom know they must make the painful decision to part, that it would not be right to have an affair just then since Tom does not wish to be entangled in the Macleans' serious marital problems; he knows Annie must settle things with Robert one way or another.
Annie understands this also and in tears, hugs Tom goodbye. Although part of her wishes she could stay on the ranch permanently, deep down inside, she knows she cannot, that Grace needs her, she must bring Pilgrim home again, and that her true home is in New York City. She understands that she would not be happy living a ranch life for long. In addition, she knows that yes, she must settle things with Robert and decide whether to continue this sham of a marriage or divorce Robert and raise Grace singly.
Tom watches a tearful Annie start back home, and fears that Grace and Pilgrim's accident has forced her to face her own emotional scars.
Tom Booker: Sometimes what seems like surrender isn't surrender at all. It's about what's going on in our hearts. About seeing clearly the way life is and accepting it and being true to it, whatever the pain, because the pain of not being true to it is far, far greater.
Annie Maclean: Look, please don't do the shucks, maam thing again, Mr Booker...
The main character, according to writer Nicholas Evans' website faq, is modeled after horse whisperer Tom Dorrance, Ray Hunt and, in particular, their younger disciple Buck Brannaman. Brannaman also doubled for Robert Redford in the film and served as the consultant. Evans himself said, "Others have claimed to be the inspiration for Tom Booker in The Horse Whisperer. The one who truly inspired me was Buck Brannaman. His skill, understanding and his gentle, loving heart have parted the clouds for countless troubled creatures. Buck is the Zen master of the horse world.
The horse training methods shown are not entirely without controversy. While Brannaman was the on-site technical consultant, he did not have creative control. Some argue that the training depicted in the film, particularly the methods of hobbling the horse and making it lay on the ground, more closely resemble the more gimmick-laden methods of Frank Bell than of a true natural horsemanship model. The constraints of filmmaking also required a number of sequences to be edited for length, and thus not showing some critical training elements that would normally be used. A few basic safety problems in the film include Redford kneeling in front of a horse known to charge humans in one scene, and wearing a large ring on his finger while training in another, a risky practice in the real world when simultaneously handling a dangerous horse and a rope.
A fundamental literary device used that goes against basic horse psychology was that of having Pilgrim, apparently a well-trained horse, suddenly became a vicious rogue following a single traumatic event. A horse may have a strong reaction after an accident if the elements that preceded the trauma are repeated at a future time (for example, it would be reasonable for Pilgrim to have developed a fear of vehicles, of crossing a road, or of climbing a steep slope), but not generally a complete change in personality, manner and outlook in the way that can occur in traumatized humans. Such behavioral changes in a horse would normally be the result of sustained, long-term animal abuse.
Some practitioners in the field of natural horsemanship have criticized the film. Followers of Pat Parelli, a direct competitor to Brannaman, claims the training methods shown in this movie are of a coercive nature, claiming that Tom Booker acts "predatory" in many scenes.
Another practitioner, John Lyons, provided a balanced critique of the film, noting that while there were many positive messages, there was also the potential for people to get some dangerous messages about horse training from certain sequences. He first noted that the multiple horses that played Pilgrim were all well-trained animals and that the movie did not represent a real-life time frame for training a single real-life animal. He pointed out that the film made the rehabilitation of the horse appear to be a one-session event, when in reality it would take considerable time for such a change to occur. Lyons criticized a number of dangerous practices shown in the movie, and was particularly critical of scene where Booker hobbles, ropes, and lays the exhausted horse on the ground, then has Grace get on the recumbent horse, which is then allowed to rise, and the horse and girl miraculously are both cured of their fears and once again a horse and rider team. He argued that the actual real-life practical risk of injury to horse and human in such a method is considerable, that a horse pushed to exhaustion is not "trained," and pushing a fearful rider in such a fashion is ill-advised. However, Lyons' critique also recognized the limitations of Hollywood filmmaking, stating, "In order to tell a story, things are often done that would be imprudent for horse owners to attempt.