It is 1757, the French and Indian War, and the British have been fighting the French for territory in North America for three years. Indian tribes fight on both sides and the colonists are caught in the middle. Three men, Chingachgook (Russell Means
), his son Uncas (Eric Schweig
), and adopted white son Hawkeye (Daniel Day-Lewis
), visit the frontier home of the Cameron's; John (Terry Kinney
), Alexandra (Tracey Ellis
), and James (Justin M. Rice
). Colonist Jack Winthrop (Edward Blatchford
) tells Hawkeye that he is gathering volunteers to fight for the British army in hopes that their homes on the frontier will be guarded against Huron war party attacks, loyal to the French. He and a group of others leave the next morning for Albany in New York to obtain these terms of agreement from General Webb. Webb agrees to grant them leave if their homes are attacked. Satisfied, Winthrop and the others agree to lend their services in the militia and join the British forces at Fort William Henry, sixty miles north of Albany.
Meanwhile, Cora Munroe (Madeleine Stowe
) and her frail, younger sister Alice (Jodhi May
), travel along a forest trail accompanied by a British garrison to see their father, Colonel Edmund Munroe (Maurice Roëves
), having received notice to meet him there. The garrison is commanded by Major Duncan Howard (Steven Waddington
) who is betrothed to Cora. Their route to Fort William Henry is led by a native guide named Magua (Wes Studi
) who acts distant towards Duncan and expresses dissent towards the British in his native language, though Duncan is unaware that anything is amiss. Magua then, without reason, turns and walks toward the back of the formation and the garrison is suddenly ambushed by a Huron war party. The women are knocked off their horses and huddle in the undergrowth together as they watch helplessly as the British soldiers are overtaken. At that moment, Chingachgook arrives with Uncas and Hawkeye and fight off the remaining Huron. Magua himself takes aim at Cora but Hawkeye forces him to flee into the forest. When the dust settles, only Cora, Alice, and Duncan are left alive. Hawkeye filters supplies from the dead and assures the survivors that he and his companions will escort them to Fort William Henry. Uncas sends off the remaining horses, explaining that they're too loud and easy to track. The party sets off on foot.
En route, Duncan questions Hawkeye and the reason he and his band were traveling west instead of fighting in the militia. Hawkeye explains that he's no scout or militia man, implying that he takes no orders. They soon all come to the Cameron's farm where Hawkeye discovers the inhabitants murdered and the cabin burned. Hawkeye and Uncas note that nothing was stolen and they come to a conclusion that a war party was responsible and are most likely scouring the frontier for hapless colonials. To Cora's astonishment, Hawkeye refuses to bury the dead but assures her that they are not merely strangers to him. Later that night, as they camp, Hawkeye explains to a contrite Cora that if they had buried the Cameron's anyone looking for their trail would see it as a sign of their passing. He speaks with her about how he was found by Chingachgook at a young age after his family was killed and raised as a Mohican and tells her a folktale about the creation of the stars, supposing that therein lies a monument to the Cameron's and his family. He finds an understanding soul in Cora and keeps watch through the night. A Huron hunting party comes close and they ready their defenses, but the party turns back since Hawkeye camped on burial grounds. They are followed by the party through the next day as they near the fort. When they arrive, they find it being bombarded by French cannon fire.
They sneak into the fort where they are welcomed and the girls reunited with their father. He is astonished to see them there and maintains that he never sent word for them to come -- Magua had tricked them into joining their father. Grateful to the trappers, he offers them whatever they need, including gunpowder and food. Munroe explains their current situation: the French are persistent and dig trenches daily that, when close enough, will allow range for mortars to bombard the fort. They have three days at best. Having heard that his previous couriers failed to deliver pleas for reinforcements, Munroe decides to send out one more to General Webb (Mac Andrews
) at Fort Edward as a last resort. When Hawkeye delivers the troubling news that innocent colonists are being attacked in the frontier, Munroe reacts with disinterest and even Duncan refuses to acknowledge what he saw at the Cameron farm. Winthrop and other militia are angered to hear Munroe's indifference to the colonists and demand to go home to tend to their families, but Munroe threatens them with sedition and commands that anyone seen deserting will be shot on sight. Hawkeye surmises that if the colonists receive no help from the British, they should go to the French. Munroe claims treason but Hawkeye assures him it's nothing but the truth. Munroe dismisses everyone.
Magua returns to the French encampment just outside the fort and addresses General Montcalm (Patrice Chéreau
), giving him the latest updates. When asked why he was targeting Munroe's children, Magua explains his deepest hatred for the man and says that he will kill the women and show Munroe that his bloodline has ended before ripping his heart out. It is later revealed that Munroe was the one responsible for an attack on Magua's village that resulted in the deaths of Magua's children. Magua was sent into slavery and by the time he was able to return to his wife, discovered that she had remarried, thinking him dead.
Later, when Cora again meets with Hawkeye in the infirmary, she realizes that she is falling in love with him. When Duncan comes to her, assuring her that all that has happened will be forgotten once they return to England, she dismisses his marriage proposal on the grounds of morality, having witnessed his lies about the Huron war parties attacking the colonists. She sends him off as a man with admirable qualities, but with none she holds highly. She later meets with Hawkeye and the two share a moment of passionate love.
Days pass without reinforcements and it's soon discovered that Hawkeye assisted his colonist friends in abandoning the fort. He is arrested for sedition and sentenced to hang. When Cora questions him, asking why he didn't leave too, he claims his only interest remains in the fort: her. She confronts her father, proudly asserting her beliefs that, maybe, the British do more harm to the colonists than good. The fort is soon overrun by the French and Munroe is forced by Montcalm to surrender. The British are allowed to leave the fort with their families to Albany, on condition that they return to England. Reluctantly, Munroe accepts but only after seeing an intercepted letter from General Webb, explaining his refusal to send aid.
The British march away from the fort defeated and are quickly ambushed again by a large Huron force led by Magua. Magua seeks out Munroe and personally cuts out his heart, telling him that his daughters are next. Hawkeye is freed by Chingachgook and they take Cora, Alice, and Duncan with Uncas away from the fighting to a cave behind a waterfall. Their gunpowder wet, Hawkeye and the others have no chance to defend themselves if they are found. With Hurons approaching, Hawkeye promises Cora that he will come back to find her, as long as she stays strong. Uncas' feelings for Alice, having grown over time, are evident as he, Chingachgook, and Hawkeye leap into the waterfall. Duncan and the women are then captured by Magua and his men.
The captives are taken to a Huron village where Magua discusses with the Sachem (Mike Phillips
), or elder, what he intends to do with them. He is then interrupted when an unarmed Hawkeye walks into the village. He is beaten down by Huron warriors as he approaches but maintains a peaceful demeanor. With Duncan translating into French for Hawkeye, he pleads with the Sachem to reconsider what Magua has told him and convinces him that Magua is simply acting out of selfish fulfillment rather than for the good of the tribe. The Sachem renders his decision: Cora is to be burned alive to atone for the loss of Magua's children. Duncan is to be sent back to the British to placate them and Alice is to be given to Magua as a bride so that both their bloodlines can continue. Hawkeye is to be released for his bravery but he speaks again the Sachem's decision, pleading with Duncan to translate that he will take Cora's place instead. However, Duncan purposefully mistranslates so that he, not Hawkeye, is taken to be burned alive. He tells Hawkeye to take Cora as Magua resentfully leaves with Alice and Duncan is taken away. Hawkeye takes Cora into the forest where they are reunited with Chingachgook and Uncas. There, Hawkeye takes aim and mercifully shoots Duncan to spare him further pain as he's burned on the stake.
Uncas immediately runs ahead of the others in pursuit of Magua's band, set on rescuing Alice. He manages to kill several members of the group before facing Magua. However, Magua quickly dispatches Uncas by stabbing him in the side. Uncas looks at Alice, apologetic, before Magua slits his throat and throws his body over the cliffside. Chingachgook and Hawkeye see this and, in a rage, Chingachgook charges ahead. Magua then motions for Alice to rejoin him as she looks at Uncas' body over the edge. She moves away and, as Cora watches, throws herself off the cliff to join Uncas in death. As Chingachgook races ahead to face Magua, Hawkeye covers his trail, shooting any Huron who comes in his way with deadly accuracy. Chingachgook and Magua face off with Chingachgook coming out the victor and effectively avenging his son. After a ritual for Uncas, Chingachgook tells Hawkeye that this land is not meant for his kind anymore and that it will be lived upon by those like Hawkeye, Cora, and their children. He then says a prayer to the spirits and asks his family to be patient in death and wait for him, the last of the Mohicans.