During a US Civil War battle in Tennessee, Union Army Officer Lieutenant John J. Dunbar ( Kevin Costner ) learns that his injured leg is to be amputated. Seeing the plight of fellow soldiers with amputated legs, Dunbar refuses amputation and steals a nearby horse. He attempts suicide by riding a horse across the line of fire, between the opposing Union and Confederate positions, who have been in a stalemate for days. His action has the unexpected effect of rallying his comrades, who storm the distracted Confederates and win the battle . After the ensuing battle, an experienced general's surgeon saves Dunbar's leg. The commanding officer recognizes Dunbar as a hero and gives him Cisco, the horse who carried him in battle, and offers Dunbar his choice of posting.
Dunbar, anxious to see the American frontier before it disappears due to mass settlement from the East, requests transfer west. After meeting with Major Fambrough ( Maury Chaykin ), who has slipped into delusions of grandeur (apparently believing he is a king and Dunbar a medieval knight), he is paired with a drayage teamster named Timmons ( Robert Pastorelli ), who conveys Dunbar to his post. Immediately after Dunbar meets leaves with Timmons, Fambrough commits suicide with his pistol.
After a scenic journey, Dunbar and Timmons arrive with fresh supplies at the desolate Fort Sedgwick, finding it deserted except for a lone wolf that Dunbar later befriends and dubs Two Socks, because of the coloring of its front legs. Dunbar, while waiting for reinforcements to arrive, sets about bringing order the deserted post, left in complete disarray by its previous occupants. Meanwhile, Timmons, while returning to their point of departure, is ambushed by Pawnee Indians and scalped. Timmons' death and the suicide of the major who sent them there prevents Union officers from knowing of Dunbar's assignment to the post, effectively isolating Dunbar. Dunbar remains unaware of the full situation and its implications. He notes in his journal how strange it is that no more soldiers join him at the post.
Dunbar initially encounters Sioux neighbors when the tribe's medicine man, Kicking Bird ( Graham Greene ), happens upon the fort while Dunbar bathes out of sight, and, assuming it abandoned, attempts to capture Cisco. After a naked Dunbar scares off Kicking Bird, he is confronted by an aggressive warrior named Wind in His Hair ( Rodney A. Grant), who declares that he is not scared of the white man. Wind in His Hair and his compatriots' attempt to capture Cisco ends in failure when the horse throws off his would-be thief. Eventually, Dunbar establishes a rapport with Kicking Bird, but the language barrier frustrates them. Believing that he should take the initiative in establishing communication with the tribe, Dunbar dresses himself in his Army uniform and rides out to meet them. On the way, Dunbar interrupts the suicide attempt of Stands With A Fist ( Mary McDonnell), a white woman captured by the tribe as a child and recently widowed. Eventually Kicking Bird and Wind in His Hair visit Dunbar at the fort and realize that the lieutenant wants to know where to find herds of buffalo, the first word that they share . Dunbar finds himself drawn to the lifestyle and customs of the tribe, and becomes a hero among the Sioux and accepted as an honorary member of the tribe after he helps them locate a migrating herd of buffalo, which they depend upon as a source of food , material, and clothing.
Dunbar further helps defend the settlement against a Pawnee raiding party, providing the Sioux warriors with surplus rifles and ammunition which he'd buried near the fort. He eventually is accepted as a full member of the tribe. After members of the tribe witness him playing with Two Socks, he is named Sugmánitu Taka Ob'wahi ("Dances with Wolves"; ugmánitu Taka means large coyote, the Lakota word for wolf). Dunbar falls in love with Stands With A Fist, a relationship forbidden by the recent death of her husband in battle but consummated in secret. The two eventually win the approval of Kicking Bird, who takes on the role of her father, and marry. Dunbar subsequently spends more time living with the tribe than manning his post at Fort Sedgwick. Wind In His Hair, his last rival, acknowledges him as a friend.
Dunbar's idyll ends when he tells Kicking Bird that white men will continue to invade their land in "numbers like the stars." They tell Chief Ten Bears ( Floyd 'Red Crow' Westerman ), who shows them a Conquistador's helmet that had been in his family for generations. The chief decides it is time to move the village to its winter camp. As the packing finishes, Dunbar realizes that his journal, left behind at the deserted fort, is a blueprint for finding the tribe, revealing that he knows far too much about their ways. Wearing Indian clothing, he returns to Fort Sedgwick to retrieve the journal but finds it is has suddenly been occupied by newly arrived Army troops. They see Dunbar and initially assuming he is an Indian, kill his horse Cisco and capture Dunbar.
When they recognize Dunbar as a white man, they treat him as a deserter, punishable by death. Dunbar tells Lt. Elgin ( Charles Rocket ) (whom Dunbar met earlier in Maj. Fambrough's office) that he has a journal containing his orders for his posting to Fort Sedgwick. Spivey ( Tony Pierce), one of the first soldiers to arrive at the fort, denies the existence of the journal, which he had found and has in his pocket. After further beating, Dunbar declares in the Lakota language that his name is Dances With Wolves. Army officers and a few troops set off to deliver Dunbar to Fort Hayes for execution. When they happen upon Two Socks, they shoot at the wolf, who refuses to leave Dunbar. Despite his attempts to intervene, Two Socks is fatally wounded, Dunbar is hit in the head again and the convoy moves off.
Soon after, Wind In His Hair and other warriors from the tribe attack the column of men, rescuing Dunbar. Smiles A Lot ( Nathan Lee Chasing His Horse ) retrieves Dunbar's journal floating in a stream. After returning to the winter camp, Dunbar realizes that as a deserter and fugitive, he will continue to draw the unwelcome attention of the Army and endanger the welfare of the tribe if he stays with the Sioux. Under the protests of his Sioux friends, Dunbar decides that he must leave the tribe, saying he must speak to those who would listen. His wife decides to accompany him.
As Dances With Wolves and Stands With A Fist leave the camp, Wind In His Hair cries out that Dances with Wolves will always be his friend, a remembrance of their first confrontation. Shortly afterward, a column of cavalry and Pawnee army scouts arrive to find their former camp site empty.
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