Jonah Hex fatefully meets fellow bounty hunter Slow Go Smith when he saves Hex from a murderous gang of outlaws. When Jonah accompanies Slow Go to collect the reward for killing the gang, they find the money has already been taken and innocent men have been murdered. Hex must intervene when Slow Go's life is put in danger while waiting to collect the reward money at the local inn.

When Slow Go is gunned down by a rag-tag gang, Jonah promises to avenge his death. When he is captured by the local townspeople and thrown in prison for Slow Go's murder he must scheme to avoid the noose and have his revenge.

Jonah tracks down the gang that murdered Slow Go Smith. He meets Doc Williams, who is peddling a cure-all medicine with his band of circus freaks. Hex spies on the group and sees them resurrect a dead body with Doc's own brand of "magic." When Jonah is captured by the gang, he fears that he too will end up as one of the undead.

Doc Williams divulges his macabre methods for resurrecting the famous gunslinger Wild Bill to Jonah Hex. Jonah plans his escape while Doc prepares the same potion for Hex.

Jonah Hex must band together with Doc Williams and his gang to fight violent Apaches. After most of the group is slaughtered, Jonah continues to search for the gang to discover their fate and have his revenge. When he finds the group, Jonah must face Wild Bill once and for all and determine the fate of the Doc Williams.

Jonah Hex tracks down a band of outlaws who have robbed a stagecoach and must bring the fugitives back to town. When a snow storm hits, they must stop at a farm house and the fugitives mysteriously escape. Jonah is shocked to find out that a young girl aided them in getting away, and must decide whether to track her down and punish her for her own crimes with the rest of the criminals or save her from the violent criminals and blood-thirsty Apaches.

When a gang of savage desperados rob a bank and kill the town sheriff, Jonah Hex is hired by a wealthy bank owner to find the thieves. The wealthy bank owner turns out to be the judge of the town, known as the "The Hangin' Woman." When Jonah saves a young girl from a fire and finds her father hanging from a tree, Jonah starts to suspect the judge's intentions for bringing justice to the town may be more sinister.