In September 1944, in German occupied France, Waffen-SS General Dietrich plots with other high-ranking Nazi officials to make a second attempt on Hitler's life.
In England, Major General Worden learns of the plot through the French Resistance. He and other Allied generals are worried that if Dietrich assassinates Hitler, then Nazi commanders will continue the war, and they need Hitler because his incompetence as a military commander.
In the meantime, Major John Reisman is on trial for hijacking a shipment of steaks when Worden comes and tells him that he is training twelve new convicted US soldiers for a suicide mission: namely, to assassinate General Dietrich. If Reisman refuses, Worden threatens to send him right back to trial.
Reisman returns to Marston Tyne Military Prison to select a new Dirty Dozen, again with the help of MP Sergeant Clyde Bowren. He initially selects thirteen prisoners — a baker's dozen: Sixkiller, Dregors, Deutsch, Valentine, Wright, Wells, Perkins, Le Clair, Rosen, Anderson, Baxley, Reynolds and Sanders.
Reisman and Bowren gather the selected soldiers together at a disused train station. Initially, there are thirteen of them but Rosen is insubordinate and Reisman has him taken back to prison, bringing the number back down to twelve. He trains the group, and convict Louis Valentine attempts to escape during a German air raid. However, Sixkiller and Wells capture and bring him back, explaining to Reisman he was merely sleepwalking.
Dressed as elite German soldiers, Reisman and the Dozen fly to a German-held French airfield and land, where they will take a bus. Realizing a Wehrmacht soldier who was black would give them away, Reisman has Dregors bandage his face as though wounded. However his hands are bare, and a Gestapo agent notices them and sounds an alarm, forcing the Dozen to escape in the bus.
During the chase, Wright attempts to murder Reisman but instead is shot and killed by Sixkiller. The bus driver is killed, causing a crash that killed Anderson. Because of the bus crash, they are behind schedule and Dietrich's train has already left. The men want to scrap the mission, Reisman; however, tells his men that there is a shipment of gold aboard the train, prompting them to change their minds. They agree to continue the mission, while resting in a cellar, they encounter a German patrol that ends badly because the lieutenant in command notices Dregors and a firefight starts, during which Perkins, Sanders and Baxley are wounded.
Aboard the train, Dietrich discovers that his longtime second-in-command Colonel Schmidt is suspicious of his motives. Fearing that Schmidt will out him as a traitor, Dietrich shoots and kills the other officer. The train arrives at a depot where it is met by hundreds of German troops. Arriving and taking shelter behind a stone wall, the Dozen watch in puzzlement. Reisman reveals he lied about the gold, angering his men.
Dregors contemplates disobeying orders and shooting Hitler instead of Dietrich. Reisman however convinces him otherwise and Dregors follows through, killing Dietrich with a sniper rifle. Chaos follows as Nazi officers bundle Hitler into a car and escape, while the soldiers attack the Dozen, who, rather than flee, recklessly attack the train, revealing treasury including priceless paintings and Beethoven's original piano.
They escape in the plane Hitler arrived in. During the run for the plane, everyone except for Reisman, Dregors, Perkins, Valentine and Wells are killed, although Dregors is shot in the stomach. During the trip back, Dregors dies from his wounds, and Reisman finds a briefcase tucked under a seat, containing top-secret intelligence information as well as a bag of jewels, which he agrees to split with the three remaining men.
The remaining soldiers lands in England, but they’re still in their uniforms and are held at gunpoint by a farmer who thinks they are Nazis, until Reisman speaks English. The farmer tells them of a good pub in the nearby town, and Reisman agrees to buy them all a round of drinks.
