NOTE: This spoiler was sent in by mcgowan
The movie begins with the southern army trying to track down the Yankee army during the civil war. The south is ambushed, but thanks to the sharp-shooting of Frank James (Gabriel Macht) and the distracting and at the same time clever antics of Jesse James, the south manages to pull through. The James brothers, along with their war buddies, the Younger brothers, congratulate themselves and then head on to kill off more Yanks.
They are surprised to find their army has pulled out when there are still "a lot of Yankees to kill". That's when they are told that General Lee surrendered yesterday, their side has lost and the war is over. They all quickly decide that the only thing to do then, is to head back home to their friends, families, and farms.
Things have changed when they get back to Missouri. First, the old childhood friend of Jesse James, Zee, (Ali Larter) is all grown up and--naturally--very attractive, which makes the normally debonair and charismatic Jesse James get tongue-tied.
Then there's this dead guy hanging in the middle of the town who's been lynched, supposedly for treason against the north, which now occupies the town. But actually, farmers that own a lot of land are conveniently getting killed if they don't sell their land to the well-groomed, suit-wearing, eastern fellows, Thaddeus Rains (Harris Yulin) and his secret-service organizer, Allan Pinkerton (Timothy Dalton) who both want to build a railroad across America. The James brothers don't want to sell their farm, and Frank James, a real smart Shakespeare quoting hick, finds that the railroad doesn't even need their land, but is just grabbing it up for as cheap as they can get, which is $2 an acre.
The Younger brothers don't want to sell either, and Cole Younger (Scott Caan) loses his temper and kills a couple of guys who get on his land. So the army decides to hang him, but his brothers Bob Younger (Will McCormack) and Jim Younger (Gregory Smith), along with Jesse James and Frank James decide to rescue him. They successfully pull this off, although Jesse James gets shot through the shoulder and has to hide out at Zee's, whose dad is the doctor.
A few weeks later, when Jesse James is all healed up, everyone has a little get together, during which some retaliators blow up people's houses, killing the James brothers' Mom.
To get revenge, the James brothers and the Younger brothers decide to get revenge by cutting off the railroad's supplies, even though the sheriff claims the blown up house thing was done by drunk guys. It was really the railroad guys though, and everyone knows it. Before Jesse James sets off to cause trouble, Zee begs him to stay because they've started something between them, but he wants revenge.
Thus the "James-Younger" gang sets out cleverly robbing banks, with their charming leader Jesse, winning over the public with his generosity of his stolen goods. Pinkerton and Rains struggle to stop them from blowing up the railroad tracks and robbing their banks, but the James-Younger gang is good. Pinkerton says if he had to design the perfect group of outlaws, they would be it. They have Frank James' brains, Jesse's charming and clever ways, and years of sharp-shooting experience from the war backing them up, and the spit-shined deputies and such are no match.
Leadership is a struggle in the group, because Cole Younger considers that Jesse is too full of himself and needs to cool it. Fights break out, and Jesse decides to let Cole take a hand in things. That leads to a trap set by Pinkerton and Rains, who think they finally have the gang figured out. Their next robbery is sabotaged and Jim Younger is shot and killed. Jesse decides he doesn't want anyone else killed and is tired of it, so he and his brother leave the gang and Jesse marries Zee.
The gang doesn't do as well without the James brothers. People don't respect the Younger brothers as much, and prefer Jesse's gentle handle on robberies and the "have a nice day" he gives them afterwards. Not only that, but when Jesse and Zee try to start a new life, and Jesse is arrested, people think Cole had something to do with it.
Jesse put on a train, all chained up. But he manages to trick one the the guys guarding him into showing he has a gun, then he manages to get it from him and he escapes onto the top of the train. Meanwhile, Zee and the whole gang shoots the train with a canon and they gain control over the whole train.
Jesse doesn't shoot either of Rains of Pinkerton, and Pinketon tells him that he (pinketon) would never go to Tennesee and that state is none of his business. So the movie ends with Jesse and Zee deciding they want to go to Tenn. and buy a farm.