The film opens with a man (Daniel Craig) waking up in the middle of the desert, with complete amnesia, a strange metal device cuffed to his wrist. The man -- who is later revealed to be notorious outlaw and fugitive Jake Lonergan -- attempts to smash the cuff off his wrist with a rock, to no avail. He gets his bearings and begins walking to town, suffering from a bleeding wound to his side and other bruises indicating he's clearly been in some sort of trouble.
Jake encounters a trio of bandits who, seeing his wound and the cuff on his wrist, assume he is a fugitive from a nearby penal facility and decide to bring him in for the reward. Jake makes quick work of the three, killing them all before they have a chance to capture him. A dog traveling with the bandits befriends Jake and accompanies him for the rest of the movie.
Jake arrives in the town of Absolution, Arizona in the year 1873, in the middle of the town's slow demise. Built as a gold prospecting outpost, the town's slowly been dying since the gold vein apparently ran out. The only source of income the town has left rests with Woodrow Dolarhyde's (Harrison Ford) cattle business. Woodrow's son, Percy (Paul Dano), takes great advantage of this fact and behaves recklessly in the town, knowing the townsfolk will take his abuse because they all owe their livelihood to his father. Jake makes his entrance just as Percy gets into a fight with the local saloon keeper, Doc (Sam Rockwell), who tells Percy that just because his father owns all the cattle doesn't mean that Percy can treat people the way he does in the town. Percy recklessly shoots his guns everywhere and demands Doc buy him free drinks for antagonizing him, a Dolarhyde.
Jake intervenes and puts Percy in his place. Percy tries to shoot Jake but misses and instead hits a Sheriff's Deputy. It seems the cuff on Jake's wrist either moved him out of the way of the bullet or moved the bullet away from him, because otherwise Percy would have shot Jake and not the Deputy. Sheriff Taggert (Keith Carradine) draws a line in the sand with this incident, ordering Dolarhyde's arrest and remand to the federal authorities in another town, since he just can't look the other way with a Deputy being shot.
For this first 1/3 of the film, everything plays out like a classic Western, with focus on the tension between the Dolarhyde family and the townspeople, with the Dolarhydes believing they are above the law and the Sheriff starting to pushback. Woodrow Dolarhyde's called "The Colonel" because he served in the Civil War and held that rank, though he does not like being referred to as such anymore by people who did not serve under him in the war. The Colonel indulges his son's every whim and uses his wealth and clout to continuously bail the boy out of jail. But, this time, having shot the Deputy, the Colonel is vexed trying to find a way out of this one for his son.
Jake is welcomed as a hero in town, for standing up to Percy, until the Sheriff notices a Wanted poster and realizes that Jake is a fugitive -- even though Jake has no idea who he is or what he might have done to warrant that Wanted poster. The Sheriff orders both Percy and Jake taken into custody and transported to federal officials in another town; the two end up being shackled together in the back of a prisoner stangecoach.
Meanwhile, something unseen has attacked some of the Dolarhyde ranchers and cattle, with the animals blasted to bits. During the investigation of what happened, the Colonel does not believe one of his men when he says that flashes of light and explosions killed the cattle. The Colonel notes there's been no rain for some time and believes the man is lying, so he has him strung up between two horses to torture the truth out of him. The man keeps repeating the same story, and the Colonel eventually has him dragged to death across the desert (even though it will soon be clear he was telling the truth).
The Colonel and his men rush into town to confront the Sheriff and free Percy from the prison transport. Just as the tension mounts and a confrontation comes to a head, out of the night sky strange ships zoom down blasting the town. The people of 1873 Absolution have no idea what these flying machines are -- with some thinking they are demons. People try firing rifles at these machines, but they have scoops and fishing line on them and the machines snatch people off the ground and carry them into the night sky. The design of the machines are like the cryptozoological "flying rods" that are caught on videotape...a rod in the middle, with these little undulations on the side, like an insect from prehistoric times or a bacteria magnified many times (though clearly made of metal). It appears these things are unmanned, predator-style drones since they seem too small to be piloted.
The townspeople have no luck bringing any of these things down, but in the middle of this commotion Jake sees his wrist cuff glowing and quickly realizes he can make it fire bursts of energy by using his mind. He frees himself and Percy from the prison coach, then blasts one of the flying machines down to the ground. After this raid on the town ends, the remaining townspeople (those not abducted) inspect the wreckage and try to determine what the machines are (with the dominent theory remaining "demons").
There's commotion in the saloon with blood spurting over all the windows, and then a fast-moving blur breaks through the town and heads into the desert. The townsfolk believe it was a "demon" that's injured, since they see the large, alien footprints it made and can see green blood in the sand. Perhaps this was the pilot of that crashed ship...it's still unclear if these are drones or if this was in fact an alien pilot. Jake and others decide to track the creature into the night. A motley crew of townspeople joins him, with a small boy named Emmett (Noah Riger) and a traveler named Ella (Olivia Wilde) joining them; the strangeness of a small boy and a woman going off on this adventure in the Wild West is noted by someone on screen with the line, "Great. We've got a boy, a dog, and a woman along for this!".
Jake leads the group through the desert, following the tracks, until they reach an enormous riverboat that's been turned upside down and dumped into the desert, seemingly at random. Inside the ship's been cleared out of gold. Camping for the night, the Colonel makes it clear that he's very disappointed in his son Percy, but is on this quest to get him back. Meanwhile the man who works as the Colonel's second-in-command, Nat Colorado (who is a Native American and part of the local tribe in the area), adores the Colonel because the Colonel took him into his household when his own parents were killed during the Civil War. The Colonel treats this man as a servant and shows him little respect, though the man admires the Colonel immensely. The Colonel is shown to be a very kind man in little moments with the boy Emmett, to whom the Colonel gives a knife he won in battle during the war.
The quiet is broken by an encounter with the "demon", who is seen for the first time as it attacks Emmett. The creature design is humanoid, with mostly reptellian features but with some insect and crustaceon thrown in. The aliens are bipedal, but are maybe 8 or 9 feet tall, and possess two extra arms inside their chest cavity that can be removed to handle very delicate objects. The others in the camp save Emmett by spotting the alien and attacking him...and the alien runs off into the night, with the chase continuing in the morning.
Jake, along the way, has flashes of memory...scenes of him being in a strange place, with strange lights, surrounded by people being tortured. It's later learned that Jake was abducted along with many other people and taken to the aliens' ship. The aliens are on Earth looking for gold, which is scarce on their planet and maybe even more valuable than it is on Earth. The aliens probably took the riverboat, looted it of the gold, and then dropped it in the desert. Another flashback from Jake reveals that when the aliens are in the vacinity, they have the ability to make gold melt and then float upwards...for collection by the aliens. This is what they do instead of traditional mining. Jake experienced it right before he was captured when the aliens flew over a house he was in, took all the gold he had just stolen in a heist, and killed the woman he loved.
When morning comes, Jake and the others encounter another group of bandits...but this time it's Jake's old gang, which had given up on him and believed him dead. Jake retakes his command and tells his gang to take them all back to their base camp.
Another battle with the aliens takes place, with Ella getting snatched by a flying machine. Jake valiantly heads off to rescue her by grabbing onto the flying machine. He ultimately uses his wrist cuff weapon to bring the alien craft to the ground. Ella and Jake land in a small lake. An alien soon attacks them when they are out of the water, slashing Ella. She dies soon afterwards.
Then, a Native American tribe shows up and takes everyone captive. The tribe puts Ella's dead body on a fire and dances around it. Everyone is soon stunned when out of the fire Ella emerges, naked, like a phoenix reborn. Ella then explains that she is a being from another planet...and that she was sent here to stop the aliens from doing to Earth what they did to her home world. Ella tells them that the aliens are nocturnal and are used to living in caves, so they do not like the daylight. The combined townsfolk and Native American team then decide to find where the aliens are based and draw them out into the daylight.
Ella explains that the aliens regard humans as insects and will not be prepared to defend themselves from a human attack. The alien ship is a giant mining device that looks like a towering mesa in the desert, in the middle of a canyon, with its hull matched almost exactly to the stone around it...but the ship is very deep in the ground where it is mining gold using the unique alien liquification process. The Native tribe does not want to follow the Colonel into battle, because he is "a white man", but Nat Colorado stands up for him and tells the tribe in their native language that the Colonel is a brave and honorable man and that he deserves their respect...so they agree to join the assault on the alien ship.
An action scene ensues where the Earth forces use mining explosives they had with them to blow up a large entrance bay in the alien tower (a whole where they alien flying machines were zooming in and out of). This definitely gets the aliens' attention, with a large number of foot soldiers descending from the tower to fight the humans. Nat is killed in this battle along with other townsfolk and tribesmen.
Jake makes it into the alien ship with Ella and realizes that his wrist cuff used to belong to one of the aliens...and that while the alien was experimenting on him, he managed to wound the alien with a laser cutting device and then accidentally make off with the cuff. There is a glowing device on the ship that steals humans' memories, which is how Jake became amnesiac after his encounter.
Ella ultimately take the cuff from Jake and heads upwards inside the ship's tower, where she's determined to destroy the ship and kill the aliens to avenge her people. Jake then has a run-in with the very alien he hurt with the laser cutter. That alien wants to use the cutter to harm Jake's face in return, but the Colonel shows up and helps Jake kill the alien...who is ultimately boiled under a vat of molten gold.
By hitting this gold collecting device, the Colonel and Jake set off a chain reaction that starts to destroy the entire mining operation. They then flee the ship, via a cavern that leads to an old gold mine and into the desert. Ella keeps making her way up inside the ship until she reaches the main control room. The aliens' ship looks like the inside of a cave, with glowing plants everywhere and a very organic design.
Jake and the Colonel help many humans out of the ship before it rockets out of the ground...these are the people who were snatched by the alien flying machines since the aliens came to the area to mine their gold.
When the ship is in the air, Ella uses the wrist cuff to destroy it. It explode spectacularly as all the townspeople and natives watch below.
With the aliens defeated, the movie becomes the ending of a traditional western.
Jake's past transgressions are forgiven. Percy's memory is gone, so he does not remember being a bad person. The Colonel uses this blank slate to craft him into the son he always wanted, using Nat Colorado as a sort of template since the Colonel realized that though this man was not blood, he had been a sort of unoffical surrogate son for the Colonel the whole time (and the Colonel didn't appreciate this until he died). Ella is dead for real this time, so Jake is mourning not only her but also the woman the aliens killed when he was abducted originally. The town is suddenly very prosperous because of the discovery of all that gold nearby.
The Sheriff wants Jake to stay in town, as does the Colonel, but Jake decides to ride off into the sunset to see what other adventures await him.
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