In 2029, no mutants have been born in 25 years. Logan has considerably aged due to his healing factor faltering, and the adamantium in his body is poisoning him. He works as a limo chauffeur in El Paso, Texas and spends his days hustling for prescription drugs. He and the mutant tracker Caliban take care of the nonagenarian Charles Xavier in an abandoned smelting plant across the border in Mexico. Xavier suffers from dementia that causes him to have destructive telepathic seizures, one of which injured 600 people and killed several X-Men the year prior. Logan is saving up enough money to buy a boat so he and Charles can live out on the sea.
Logan is approached by Gabriela López, a former nurse for biotechnology corporation Alkali-Transigen, who offers to pay him $50,000 to escort her and a young girl named Laura to a refuge called Eden in North Dakota. She gives him $20,000 upfront. Logan reluctantly agrees, but upon arriving to Gabriela's motel room to pick her up, finds her dead. Logan checks her phone to find an unsent text message saying "they're here" and takes her phone. He drives back to the plant before realizing Laura hitched a ride in the trunk of his car.
Donald Pierce, Transigen's chief of security with a robotic hand, shows up at the plant asking where Laura is before getting knocked out by her. When Donald comes to, he captures Caliban and surrounds the plant with Reavers. Laura reveals she has claws and healing powers just like Logan. She, Logan and Charles manage to escape. Caliban is tortured into using his powers to find them.
Charles and Logan watch a video on Gabriela's phone that shows Transigen was breeding children with DNA samples from mutants to turn them into weapons. Laura was bred with Logan's DNA, making her his daughter. The children were planned to be executed due to being hard to control, but Gabriela helped them escape.
In Oklahoma City, Logan finds Laura's collection of X-Men comics, which he tells her are all fake. He discovers one of them references Eden, which causes him to doubt that it is a real place they are driving to. The Reavers arrive, but Charles has another seizure that causes everyone but Logan and Laura to freeze. Logan kills all the Reavers in the room before giving Charles his medication, and they leave the city. Dr. Zander Rice, the head of Transigen, arrives to help Pierce.
On the highway, a truck towing horses swerves off the road, and the horses escape. Xavier uses his psychic powers to calm the horses down, and Logan helps get the truck back on the road. The Munson family- father Will, mother Kathryn and teenage son Nate- invite Logan, Charles and Laura for dinner at their house, and Charles accepts. After dinner, Logan wants to get back on the road, but the family and Charles insist they sleep for the night.
Rice unleashes X-24, a mindless clone of Logan in his prime created as Transigen's ultimate weapon. X-24 kills Charles, Nate and Kathryn and injures Will before shackling Laura and heading to the Reavers' van. Caliban grabs two grenades and sets them off, killing himself and several Reavers, but only injuring Pierce. Logan is outmatched by X-24, but Will pins X-24 with his truck before dying from his injuries. Logan and Laura escape in Will's truck with Xavier's body.
Logan buries Charles' body, then passes out from anger after the truck won't start. Laura steals another truck and takes him to a hospital before revealing she can speak. She convinces him to finish the drive to North Dakota, despite him still insisting that Eden is not real. Pierce finds out about the children's location from a photograph Laura kept.
They arrive at Eden, which is a safe haven run by Rictor and former Transigen test subjects. There, Logan learns that the children will make an eight mile journey across the forest to the Canadian border. Laura finds an adamantium bullet that Logan has kept since he escaped from the Weapon X facility, which he once considered using to commit suicide. Logan decides not to accompany them, to Laura's dismay.
The Reavers arrive and ambush the children. Logan takes an overdose of a serum given to him by Rictor that temporarily enhances his healing abilities and boosts his strength. He and Laura plow through the Reavers before the serum wears off. As Pierce holds Rictor at gunpoint, Logan meets Rice, who plans to avenge his father that Logan killed years ago at the Weapon X facility. Rice reveals that the reason no new mutants have been born in years is due to genetically engineered crops created by Transigen and distributed through the world's food supply. Logan shoots Rice with a gun and the children use their combined powers to kill Pierce.
X-24 fights Logan, who is once again overpowered by him. Rictor uses his powers to flip a truck onto X-24, but X-24 frees himself and impales Logan on a large tree branch, mortally wounding him. Laura shoots X-24 in the head with the adamantium bullet, killing him.
Near death, Logan tells Laura not to become the weapon she was made to be, and she tearfully acknowledges him as her father. Holding onto Laura's arm, Logan succumbs to his wounds and dies peacefully, with his final words being "So this is what it feels like." Laura and the children bury him before continuing their journey across the border. Before they depart, Laura tilts the cross on his grave marker to create an X.
