In central Texas, 1849, a Comanche war party attacks the McCullough household, kidnapping Eli and his brother, Martin, and killing the mother and sister. Eventually, the Comanche kill Martin when he acts out against them.
In south Texas, 1915, a grown Eli and his son, Pete, discover the body of Armando, one of Pedro García’s ranch hands. Pete confronts Niles Gilbert about the killing. Niles explains that Armando helped the Sediciosos steal Pete’s property.
Eli hosts a lavish birthday party with potential oil investors in attendance, invited by his older son Phineas. Pete worries about the ethics of convincing investors to invest in land that has no oil. In the middle of the party, Eli’s oil derrick erupts in flames.
Eli, Pete, Phineas, and ranch foreman, Tom Sullivan, capture Cesar, one of the saboteurs and Pedro’s son-in-law. Eli cuts off Cesar’s ear and demands to know who blew up his rig. Cesar confirms it was the Sediciosos but insists he doesn’t know where the rebels are heading next. At Maria García’s insistence, Sheriff Graham confronts Eli about Cesar’s disappearance but abandons his investigation after Eli offers $200 to his reelection campaign.
Prairie Flower, a Comanche woman, repeatedly beats young Eli for making mistakes with his work. When Eli finally fights back, she later sneaks into his tipi and mounts him. They become lovers.
Pete lets Cesar go and urges him to flee to Mexico. Cesar tackles Pete and gets stabbed dead in the ensuing struggle. Pete buries Cesar.
Eli and Phineas meet with a potential investor in Austin. When the investor falls through, Phineas advises Eli to sell off sections of land. Eli reluctantly agrees.
Prairie Flower tells young Eli that Charges the Enemy is planning to marry her after he pays a dowry. Knowing about Eli and Prairie Flower’s relationship, Charges the Enemy hits Eli’s cheek with an arrow during a training session.
In the present day, Eli visits an old flame, Ingrid, and makes love to her while her husband is at work.
Aniceto Pizaña, a Mexican rebel, obtains supplies from Pedro. Maria warns Pete about Pizaña’s imminent attack on a train line. Using Pete’s intel, Eli gathers a posse and ambushes the Sediciosos.
Young Eli and the Comanche come under attack from Texas Ranger Bigfoot Wallace. Eli brings an injured Comanche back to camp, saving him from being scalped, and enabling him to enter the next world upon death. Toshaway, Eli’s owner, thanks him.
Worried about the mounting violence, Pete’s wife Sally complains to Pete for not moving their family to the city as he promised years ago.
Young Eli accompanies a Comanche war party to kill the Tonkawa that are threatening their land. The war party finds the Tonkawa camp deserted, ravaged by smallpox. Eli, who is immune to smallpox, enters the camp to steal the horses. A sick Tonkawa man tries to convince Eli to bring diseased supplies back to the Comanche but Eli stays loyal to the Comanche.
Pizaña’s Sediciosos attack the McCullough household, injuring Jonas and killing Sullivan. Eli’s granddaughter, Jeannie, rides to the García ranch to seek help. Pedro and his men chase off the Sediciosos, saving the McCulloughs. Sally brings Jonas to Austin for medical treatment.
Young Eli discovers a band of white buffalo hunters and leads the Comanche to their camp, killing nearly everyone and taking the buffalo meat. Charges the Enemy kidnaps a white girl, Ingrid, and presents her to Prairie Flower’s father as a dowry.
Niles accuses one of Eli’s workers, Ramon, of leading the Sediciosos to the McCullough ranch. He convinces Charles to help kidnap Ramon. To Charles’s surprise, Niles and his men proceed to hang Ramon.
Eli notices oil on the hoof of Jeannie’s horse and realizes that she recently rode through an oil seep. He and Jeannie find the oil seep, but it’s on the García’s land. Jeannie stows a bottle of oil collected from the seep in her doll house.
In Austin, Phineas lifts Sally’s spirits by taking her to an underground gay club, where she meets his romantic partner.
Pete takes Charles to Austin in the wake of Ramon’s death. Sally worries about Charles being surrounded by men who glorify violence. Pete proposes that she and the children stay in Austin while he lives at the ranch.
Charges the Enemy pushes young Eli off a cliff then tells the Comanche that he let Eli escape. Toshaway informs Prairie Flower that her father accepted the dowry payment from Charges the Enemy. Prairie Flower sneaks out of camp to look for Eli, but Charges the Enemy tracks her down and convinces her to return to camp for her parents’ sake. Prairie Flower and Charges the Enemy get married.
Maria visits Pete at home. Pete kisses her and they make love. Maria tells Pete that her former husband left her after he learned that she could not have children. Pete proposes they run away together. She scolds him for proposing such a plan.
Eli and Phineas bribe Judge Kilbourne to help make it seem as though Pedro García hasn’t paid his land taxes in 10 years, thus casting doubt on his ownership of the land.
A prostitute named Lena tracks down Eli and shoots him in retaliation for his massacre of her Apache village in 1881. Eli survives but believes his near-death experience is a sign that he should call off the oil scheme. Phineas tries to dissuade Eli from changing his mind but Eli remains firm.
Young Eli wakes up with injuries and runs into a settler, Maggie, at her camp. Maggie nurses him back to health but then takes him hostage to cash in on a reward for white captives. Eli escapes and steals her horse, abandoning her to die. She curses him and his future sons.
Eli announces to Pete that he’s decided to sell the ranch and move to north Texas. When Eli later finds Gilbert’s Saloon engulfed in flames, he yells at Phineas for continuing with their plan despite his orders not to.
While packing Jeannie’s belongings to bring to Austin, Pete discovers the jar of oil in her doll house. He confronts Eli and Phineas and learns about their plot to tamper with Pedro’s tax records and convince Niles that Pedro burned down his saloon.
Eli declares war against Pedro and rallies an angry mob. Meanwhile, Pete warns Pedro that Eli found oil on his land and that men are coming to attack his house.
Young Eli returns to the Comanche camp and vows to kill Charges the Enemy. Toshaway reminds him that Comanche do not kill other Comanche and counsels him to accept Prairie Flower’s marriage.
Eli and his men arrive at the García household. Pete tells everyone about Eli’s scheme but Niles accuses Pete of lying. A shootout ensues, killing everyone in the García household except for Maria. Pete and Maria flee.
Rangers attack the Comanche men during a hunting expedition. Eli shoots an arrow at the Ranger who is about to scalp Charges the Enemy. Before dying, Charges the Enemy apologizes to Eli for dishonoring him. Eli scalps the Ranger.
Phineas kills Lewis, who he had hired to help frame Pedro.
In Austin, Phineas informs Sally that he last saw Pete running for the border with Maria.
Eli burns down the García household, along with all of Pedro’s property tax records. Judge Kilbourne auctions off Pedro’s land to Eli and Phineas.