Jonah Hex (Josh Brolin) narrates about his experiences with war (specifically the Civil War). Having fought on the side of the Confederacy, he went against his commanding officer, Quentin Turnball (John Malkovich) and betrayed his platoon to save a hospital full of civilians. Killing Jeb Turnball, Quentin’s son in the process, Quentin decided to exact his revenge on Jonah Hex by tying him to a cross and branding his face with a hot iron. Quentin then had his right hand man, Burke (Michael Fassbender), burn down Hex’s house with his wife and son still inside.
Days later, a tribe of Native Americans found Jonah half dead and treated him with their mystical powers to revive him. As a consequence, Jonah is present among the living while also having a presence on the other side (allowing him an affinity to crows and the ability to temporarily resurrect the dead). He carved the brand Turnball gave him off of his face with an axe, resulting in his disfigured visage. He pursued Turnball for years until Turnball was apparently killed in a hotel fire. Since then, Jonah has worked as a bounty hunter who kills the guilty and brings them back for a reward.
Jonah drags three corpses behind him on his horse. He presents them to the sheriff of the town he is visiting and tells them that he wants his reward. The sheriff tells him that there were 4 bandit brothers and that they cannot pay him if he didn’t do the job. Jonah tosses him a bag with the fourth brother’s head in it and tells him that the brother’s body was too fat to drag through the desert. Jonah notices that there are 5 coffins and realizes that they were never going to pay him. The sheriff has a sniper try and shoot Jonah but he misses twice. Jonah kills all the men and takes only the amount stipulated in the reward from the sheriff’s wallet. He then promotes the village idiot to sheriff and leaves.
On a railroad train, Union soldiers are transporting a key component of a weapon to another part of the country for safekeeping. A little boy in the passenger cart notices outlaws riding next to the train on horseback. The Union soldiers try to react but are betrayed by two turncoats in their midst (who hold the train hostage with a vest of dynamite). Burke sets up a bomb on the railroad tracks and uncouples the engine and the part of the train holding the weapon component from the rest of the train. Burke blows up the passenger and soldier cars and he presents the sole survivor to Turnball. Turnball, alive and well, orders the man’s execution and tells them to take the component to Fort Resurrection while he goes to have a chat with the informant they have in Congress.
Across the country, President Grant is informed of the train massacre by Lieutenant Grass (Will Arnett). He realizes that Turnball is planning an attack on the Union on the fourth of July (the country’s centennial). Grass is told to find Jonah Hex since Grant is aware of Hex’s infamous quarrel with
Jonah is in a bar drinking when a man tries to start trouble. Jonah shoots him when the man asks what happened to his face. He then leaves the bar. Lilah (Meghan Fox) has just finished having sex with her latest client. The client insists that he will leave his family for her if she agrees to go to the city with him. She tells him to leave but he keeps being more and more insistent. She pulls a gun on him and tells him to leave. She puts her payment in a box with the rest of her earnings. She hears a knock on the door and assumes it’s the client again but is happy to see that it’s Jonah. The two spend the night together and it’s clear that Lilah is drawn to the disfigured man for more than a professional interest (he doesn’t pay).
The next morning, Hex prepares to leave and she asks him why he never considers her when he leaves on the road. He tells her that there is no life for them since everyone he loves dies. She gets upset and tells him that one day he’ll come back and find that she’s gone just to know how it feels. Grass’s men burst into the brothel at that moment and tell Jonah that he is being conscripted into the nation’s service to track down Quentin Turnball. Jonah is prepared to shoot the messenger for saying Turnball’s name but when he’s told that Turnball is alive, he realizes that he did not avenge his family.
Turnball meets with his informant, Adelman Lusk (Wes Bentley) and forces him to tell Turnball where the key component of the weapon is being held in exchange for a position in Turnball’s new world order once his plan succeeds. Turnball and Burke go and find the component, a chemical orange ball, which Eli Whitney helped develop in order to help the Union win the war. It was never used because of how destructive it was. Turnball has the equipment taken to his base.
Jonah meets with Grass and Grass tells him that Turnball is trying to build nation-killing weaponry. Grass explains that the trail went dead because their informant died. Jonah goes to speak with the informant and resurrects him with his touch. While the process brings the dead back, they start to burn up the longer he holds onto them (and they burn up faster the less time they’ve been dead). He asks where he can find Turnball but learns that the man hadn’t been recruited by Turnball, but another associate of Hex’s who betrayed his family: Colonel Slocum (Tom Wopat). Jonah puts some dirt on the corpse’s head to ease the burning and thanks him. The informant hears dogs barking and Jonah tells him that the Hell Hounds are coming to take him away. The informant has a look of fear on his face until Hex lets go and the man decomposes again. Grass is skeptical that Hex learned anything but Hex goes on his way.
Jonah goes to pay Colonel Slocum a visit at his illegal death match pavilion. He asks Slocum where Turnball is but Slocum tells Jonah that it isn’t too late to overthrow the Union. Jonah tells Slocum that he’s going to die after he learns what he wants. Slocum tells Jonah (sarcastically) to ask Turnball’s dead son, Jeb, where his father is. Jonah throws Slocum into the death match pit where the crazed fighter, Snake Venom, attacks and kills him. Jonah leaves the tent and kills some of Slocum’s men, saving a dog, which follows Jonah around.
Jonah, his horse, and the dog go to Gettysburg. Jonah spends the night digging up Jeb’s corpse and uses his resurrection abilities to revive him. Jeb (Jeffery Dean Morgan) attacks Jonah several times but Jonah just lets go (causing Jeb to turn into a skeleton again). Jonah finally gets Jeb to stop and the two talk. Jonah apologizes for having to kill Jeb and tells him that he’s sorry. Jeb bitterly tells Jonah that he and his father are exactly alike from where Jeb is observing. He tells Jonah about Fort Resurrection and that Jonah better stay alive as long as possible since there are people in the underworld who are waiting for Jonah to die so that they can have their way with him. Jeb gets back in the ground and Jonah buries him again telling him that soon Jeb will have company.
Jonah pays a visit to Smith (Lance Reddick), a gunsmith, and buys a pair of dynamite crossbow launchers. Smith points out that Jonah’s hatred of the Union isn’t born out of Southern loyalty but out of a stubbornness to adhere to the rules of government. He asks why Jonah continues to hate freedom when he doesn’t support slavery or secessionist principle and tells him that on the fourth of July, he’s going to celebrate the birth of the nation with his two boys in the capitol.
Lilah’s obnoxious client comes by again and tells her that he owns her now. She goes for her gun but sees that the client has taken it. He tells her that he informed Grass’s men of where Jonah was and that he isn’t coming back. He attacks Lilah and she stabs him in the chest with a knife she hid under her bed.
Jonah goes to Fort Resurrection and sees the plans for the machinery. He encounters Turnball but doesn’t get a chance to kill him. Turnball escapes and has Burke fight Jonah. Jonah gets shot several times and is dragged out of the fort by the dog. He jumps onto his horse and escapes just as Burke throws a stick of dynamite at him. Afterwards, Burke and Turnball discuss the situation and decide to move locations. Turnball tells Burke to find what Jonah loves and bring it to him so that Turnball can kill it in front of Jonah.
Jonah collapses near death and imagines what it would be like to fight Turnball. The Dog drags him back to his Native American allies and they perform a ceremony on Jonah to resurrect him. A crow forces its way out of Jonah’s mouth as he is healed and Jonah returns to the land of the living ready to kill Turnball. He goes to a telegraph office and relays a message to Washington about the stakes and Turnball’s plan to attack the capitol. As Jonah rushes to find Turnball, Burke pays Lilah a visit and kidnaps her.
Hex arrives at the dock where the ship is being prepared. Burke attacks him and the two fight without any of Turnball’s men noticing. Hex kills Burke for his family then resurrects him and utterly destroys him by burning him up. Jonah goes to shoot Turnball but Turnball pulls Lilah out and Jonah is forced to surrender and knocked out.
Turnball places Jonah and Lilah in the hold of the ship and tells Jonah that he wants him to watch as Turnball destroys the Union and then Lilah. Lilah picks her handcuffs and gets Jonah out of his handcuffs so that he can go and kill Turnball. Lt. Grass tries to stop Turnball’s ship with his Ironside but Turnball blows it to hell with the Nation Killer. Jonah and Turnball fight and fall from the ship’s top into the engine room. Turnball gains the upper hand but Jonah slowly turns the tide. Turnball gives the order to destroy the city and the preliminary weapons are fired, laying the preparation for the chemical bomb. Lilah takes Jonah’s axe to kill the man operating the weapon but he knocks it from her hand and it falls into the engine room. As the chemical is about to be deployed, Jonah whips the axe to jam the mechanism, stopping the bomb. He then beats Turnball brutally and forces his neck into a gear, trapping Turnball. He goes up to the upper deck and saves Lilah. The pair jump into the ocean just as the chemical ball ignites in the engine room, killing Turnball and all his men.
The next day, the President rewards Jonah for his services with money, a full pardon and a job offer. Jonah turns down the offer for sheriff of the United States and tells the President that if they need him, they’ll be able to find him. He and Lilah walk off into the sunset.
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