In the year 1873, in the rugged Arizona Territory, an unnamed loner, Daniel Craig, awakens in the desolate desert, injured and devoid of memories, sporting a perplexing metal shackle on his wrist. After defending himself against three drifters attempting to rob him, he acquires their clothes, weapons, and a trusty horse. He stumbles into the small town of Absolution, where the local preacher, Meacham (Clancy Brown), tends to his wounds. When the stranger subdues the unruly Percy Dolarhyde (Paul Dano), a drunken menace to the town, Sheriff Taggart (Keith Carradine) identifies him as the infamous wanted outlaw Jake Lonergan and attempts to take him into custody. However, Jake fights off the posse and nearly escapes, only to be knocked out by a mysterious woman named Ella Swenson.
Colonel Woodrow Dolarhyde, Percy's wealthy and ruthless father, storms in with his men, demanding the release of his son and Jake, accusing Jake of stealing his gold. In the midst of their standoff, an alien craft falls upon the town, attacking the inhabitants. Percy, the sheriff, and several townsfolk are seized by the alien ship’s long, whip-like tendrils. In a remarkable turn of events, Jake’s shackle transforms into a weapon, adeptly shooting down one of the threatening ships and halting the attack.
With Dolarhyde, Ella, and the townspeople, Jake joins a posse determined to track down an alien that managed to escape the downed vessel. Meanwhile, Jake recalls a disturbing memory of returning to an abandoned cabin with gold shortly before he and a woman, Alice (Abigail Spencer), were abducted by the aliens. As the posse camps in an overturned paddle-wheel steamboat during the night, tragedy strikes when the alien they were following kills Meacham, who heroically sacrifices himself to save Emmett (Noah Ringer), Taggart's grandson.
As dawn breaks, many members of the posse have fled, and the remaining ones face an onslaught from Jake's former gang, who seek to reclaim their stolen loot. Amidst the chaos, aliens launch another attack, capturing Ella. In a daring move, Jake boards the alien ship to confront the pilot, causing a crash but leaving Ella gravely injured.
Before long, the posse finds themselves in the hands of the Chiricahua Apache Indians, who blame them for the alien chaos. In a shocking revelation, Ella is resurrected from the flames by a Chiricahua warrior, disclosing her true identity as an alien sent to help humanity resist their invaders, who have obliterated her home world. The aliens have been abducting humans for experiments and mining gold to fuel their technology. Despite their strength, the aliens are not invincible: Jake’s gauntlet holds the potential to defeat them, along with traditional means like stabbings and gunfire. Ella divulges that Jake possesses critical knowledge concerning the aliens' whereabouts, urging the group to thwart their extermination of humanity.
With newfound determination and clarity in his memories, Jake remembers the tragic fate of Alice, who was euthanized after being a subject of alien experimentation. Armed with this vital information, Dolarhyde leads the group in preparations to assault the aliens’ mothership. Jake rekindles ties with his old gang, convincing them to join the resistance. In a bold sneak attack, they breach the spaceship by obliterating the shuttle bay, compelling the aliens into a ground battle. Jake and Ella infiltrate the ship, liberating the captives, though Jake is captured in the process. After a daring rescue by Dolarhyde, both men take vengeance on the alien responsible for Alice's death and narrowly escape the spacecraft as it prepares to launch.
In an act of bravery, Ella sacrifices herself to destroy the alien ship using Jake’s powerful gauntlet. With Jake's memory partially restored, some townsfolk also begin to recall their lost past. Acknowledging his status as a wanted man, Jake chooses to leave the town behind. Sheriff Taggart and Dolarhyde promise to claim he perished in the alien invasion, while the citizens harbor hopes of rebuilding the town, anticipating that the newly discovered gold mine will attract settlers. Graciously declining Dolarhyde's offer to help rebuild, Jake rides away into the horizon, seeking his own path.
