The Western & Atlantic Flyer "speeds into Marietta, Georgia in the Spring of 1861," pulled by the locomotive "General." The engineer, Johnnie Gray (Buster Keaton) gets down to oil around, and is observed by two admiring boys. He has two loves: his engine and his girl. The two boys follow him when he goes to call on Annabelle (Marion Mack). They follow him right into her house, and he has to trick them to get them to leave. He presents Annabelle with a portrait of himself in front of his engine. Annabelle's brother (Frank Barnes) arrives with the news that war has broken out. He and their father (Charles Smith) go to enlist. Annabelle expects Johnnie to enlist, so he says goodbye. She gives him a kiss, and he backs off the edge of the porch.
Johnnie runs by a shortcut and vaults a counter to be first in line. He doesn't hear that he is "more valuable to the South as an engineer," so he doesn't understand why he is rejected. He tries two more times to sign up, but is kicked out the door. Annabelle's father and brother invite him into the line, but he has had enough. They think he is a disgrace, and tell Annabelle he never got in line. He sits dejected on his engine's siderod. Annabelle tells him she won't speak to him until he is in uniform. An engine hostler moves the engine, with Johnnie still sitting on the siderod. He doesn't notice until, on the third revolution, the locomotive is entering the enginehouse.
One year later, in Chattanooga, Gen. Thatcher (Jim Farley) and his "chief spy" Capt. Anderson (Glen Cavender) hatch a plan to take a group of spies to steal a train at Big Shanty and drive it north, burning bridges to cut the supply line to the Confederate army threatening Chattanooga.
At Marietta, Annabelle boards Johnnie's train to visit her wounded father. Johnnie sees her pointedly fuss with her brother's medals. When the train stops at Big Shanty for breakfast, Anderson and his men get off on the side away from the station. Annabelle gets into one of the boxcars to retrieve money from her trunk. The men remove the coupling pin between the boxcars and the coaches, get aboard, and start the engine. They discover Annabelle, and have to take her. Johnnie calls for others to follow him, as he runs after his train, but they soon give up running.
The Yankee spies tie up Annabelle. They stop to cut the telegraph wires, and back at Big Shanty, the operator notices the line go dead. Johnnie stops at a handcar shed, and only then notices that no one has followed him. But he gets the handcar going. The spies remove a rail and jam stones in the guardrail. Johnnie falls off the handcar, which runs off the track and smashes down an embankment. The "General" speeds past Kingston, where the "Texas" waits on a siding. Johnnie sees a bicycle, which he leaps on, but it doesn't work well along the rough roadbed. On the "General," Capt. Anderson unpacks a Confederate uniform. Johnnie runs into Kingston and shouts for help. Soldiers pile onto the flatcar behind the "Texas." Johnnie pulls the pin behind the flatcar to leave the rest of the train, but the flatcar is not coupled to the locomotive, and when he speeds away he does not notice the flatcar full of soldiers is left behind.
By the time he notices he is alone, Johnnie sees a railroad mortar on a siding. The Yanks have stopped for water and wood. Johnnie is pulling the mortar car. The spies see him, and pull away without shutting off the water, and Johnnie gets an unexpected shower. Capt. Anderson won't stop and fight because he assumes they are outnumbered. They chop through the rear wall of the end boxcar. Back on the mortar car, Johnnie loads one handful (and a bit more) of powder, wadding, and a cannonball into the mortar, aimed to arc over the engine and hit the spies. He lights the fuse, and hurries back over the tender to the engine. The mortar fires, and sends the cannonball in a short arc right into the cab. Johnnie rolls it out of the cab and returns to the mortar. As he prepares another shot, there is a huge explosion beside the track back down the line. This time he puts the whole canister of powder in the gun. In hurrying back to the cab, his foot gets caught in the coupling bar, and dislodges it. When he finally gets his foot unstuck, the bar falls down and bangs against the crossties. The jostling makes the mortar lower until it points right at Johnnie, who has now got his foot caught in a loop of chain. He gets free, and scrambles all the way to the cowcatcher. The two trains enter an S-curve, and are at just the right places when the mortar fires that the shot misses the "Texas" and explodes just behind the spies.
The Yanks release the rear boxcar to leave it in Johnnie's way. He pushes it onto a passing siding and proceeds. Busy feeding the fire, he doesn't notice that the boxcar continues to roll to the end of the siding and back onto the main track. He can't figure out how the boxcar got in front of him again. From the remaining boxcar the Yanks drop timbers across the rails. Johnnie, looking for a cloth to handle a leaky valve, doesn't see when the boxcar hits one of the timbers and is derailed out of the way. He can't figure out why the boxcar is now gone.
Now he can see the timbers on the track. He slows the engine, and runs ahead to lift the first one. But he stumbles, and falls back onto the moving cowcatcher, holding the timber. With adroit timing, he uses it to hit the next one out of the way.
The Yanks throw a switch to a spur track, and lift Annabelle over the tender to the engine cab. Johnnie, occupied with firewood again, sees just in time to stop before the end of the spur track. He backs out of the siding, and starts the engine forward, but the wheels slip. He gets down to throw dirt onto the rails. He doesn't notice when the wheels get a grip and the engine pulls away. He has to run to jump on the back of the tender.
The Yanks have started a fire in the remaining boxcar, and they leave it in a covered bridge. Johnnie arrives in time to push it out. But there is so much smoke in the cab that he retreats to the tender deck, where he sits on the water hatch, not having noticed the lid is not on. He finally diverts the burning car onto a siding.
Johnnie is so busy chopping wood on the tender he does not notice the Confederate army retreating. The Union army now passes, and Capt. Anderson removes his Confederate uniform. Johnnie finally notices the Union soldiers, and crouches down on the floor of the cab.
The "General" passes under a trestle, and loops around to stop on the trestle above. When Johnnie passes below, the Yanks drop timbers down on him. Some land on the tender, providing fuel. But Capt. Anderson gets a good look, and says, "There is only one man on that engine." Johnnie stops, and gets off to hide in the woods. It starts to rain.
When night falls, Johnnie climbs through the window of a house and takes food from the dining table. When a number of Union officers enter, he hides under it, and hears them planning to get supply trains across the Rock River bridge so the army can attack the Confederates the next day. One officer's cigar burns a hole in the tablecloth, and Johnnie is able to see when Annabelle is brought in and locked in the next room. The officers leave. Johnnie knocks out a sentry with a log and steals his uniform. He knocks out another sentry with his rifle butt, and climbs in the window of Annabelle's room. He gets her through the window, and leads her into the forest. They encounter a bear, and both get stuck in a bear trap. Johnnie keeps losing Annabelle, so he decides they should stay in one place until dawn.
The next morning, Johnnie sees his locomotive. He empties a large sack of boots and stuffs Annabelle into the bag. Then he realizes one of his own shoes has come off and he has to find it among all those on the ground. He joins a line of soldiers loading the boxcar behind the "General." He stands where Annabelle can reach to uncouple it from the rest of the train, then puts her into the boxcar as a bag of supplies. He cringes and covers his eyes when he sees a crate and a barrel tossed in after her. He joins the line loading firewood, knocks out the officer in the cab, and starts the engine, heading back south.
Johnnie stops outside of town, loops a rope over a telegraph pole, and ties it to the boxcar. When he pulls away, the pole and wire are pulled down, and the telegraph line is cut. He chops the rope, leaving the pole across the track. From the tender, he chops through the front wall of the boxcar, climbs in, and searches for Annabelle. He finds her among all the freight only when he steps on the sack she is in. Then he has to help her get across to the tender.
Johnnie stops to throw fence rails onto the tender for firewood, but he has some difficulty getting them to stay there. Meanwhile, the Yanks have given chase with the Texas and another engine. They have to stop to get the telegraph pole out of the way. Annabelle takes what is left of the rope, and ties it across the track between two young pine trees. Johnnie almost leaves without her. When she shows Johnnie what she has done, he demonstrates how ridiculously flimsy it is. But the Yanks are coming, and they scramble into the engine cab and start off. The rope pinions the soldiers riding the "Texas" and the two trees are uprooted and get caught up in the siderods. Annabelle's arrangement has succeeded in forcing the pursuers to stop once more.
Johnnie knocks out the whole back wall of the boxcar. The Yanks have to stop again to clear it off the track. He slows them down by tossing all the freight onto the track out the open back. In the cab, the Union officer is just regaining consciousness. Johnnie returns just in time, knocks him out with a well-aimed log, and takes his pistol.
They stop at a water tank. Johnnie does not notice he has pulled the spout away from the supply pipe. When he opens the valve, Annabelle is knocked down by the deluge. He replaces the spout, and she gets more water over her. They leave, the water still flowing, and it drenches the officers on both the chasing trains.
Annabelle feeds the fire. She sees a log with a big hole in it, and rejects it, tossing it out of the cab. Johnnie can't believe it. The Yanks plan to couple to the rear of the boxcar. Annabelle sweeps the cab; Johnnie tosses the broom. Annabelle feeds the fire with kindling; Johnnie picks up a sliver and hands it to her. She tosses it in the firebox. He shakes her, then kisses her.
The Yanks catch up, and couple to the rear of the boxcar. At the forward end, Johnnie uncouples it. The Yanks fire at him. They switch the boxcar into a siding, then back out onto the main track. The second train smashes into them, knocking down officers. They just get re-seated when the train starts with a lurch, and they tumble again.
Johnnie fastens a chain between the tender and some switch points. He has Annabelle start the engine, and the chain deforms the switch points. But Annabelle cant stop the engine. Johnnie runs downhill to meet her where the track passes below, but she gets the locomotive reversed, and he has to scramble back up the hill. They meet the Yanks at the broken switch, where the two Yank trains end up on an elevated spur track, smashing again, allowing Johnnie and Annabelle to get away.
Johnnie sticks the end of a fence rail in the fire. He stops in the middle of the Rock River bridge, and piles firewood on the ties behind the tender. Meanwhile, the Yank officers can't figure out how to fix the switch so they can continue the pursuit, and a Union army is approaching the rendezvous at the bridge. Johnnie pours kerosene from the headlamp onto the firewood. Annabelle knocks the burning fence rail off the tender, and Johnnie is trapped on the far side of the fire in the middle of the bridge. He jumps over the fire just as Annabelle moves the engine forward, and Johnnie falls through a gap into the river.
The Yank officers are still ineptly dealing with the broken switch. Johnnie hails a Confederate picket, and is fired at. Annabelle points out that he is still wearing the Yankee uniform, so he changes. They pull into Marietta, with the whistle blasting, and Johnnie runs to the Division Headquarters to warn them of the attack. The General leads the army out of town, and Johnnie and Annabelle find themselves in the middle of a stampede of traffic. Annabelle sees her wounded father, and Johnnie is left in the deserted street. He finds a sword belt and pistol, straps them on, and follows the army.
The Yank officers are still trying to fix the switch. A locomotive engineer pushes his way through them and does a neat, quick fix using an ax. The two engines reach the Rock River bridge at the same time as the Union army arrives. The General says, "That bridge is not burned enough to stop you, and my men will ford the river." The "Texas" proceeds onto the bridge, the span collapses, and the engine crashes into the river.
The Confederates surprise the Union army, and a fight begins. Johnnie is near an officer, and he imitates his commanding gestures, but his sword keeps coming apart. He stands near a gun battery, where a sharpshooter keeps picking off the artillerymen. Finally Johnnie's broken sword is effective. At his commanding swing, the blade comes off again and spears the sharpshooter. Johnnie tries firing the unmanned cannon. He has to yank the firing lanyard so hard that the gun tilts straight up before firing. He retreats, but the shot lands in the river, blowing a dam. The surge of water catches the Yankee infantry in the river, forcing them to retreat. Johnnie directs the other artillerymen to fire at officers on the remaining train. They retreat, and the whole army retreats. Johnnie directs another shot that derails the last car, stopping the retreating supply train. Johnnie saves a battle flag, and mounts a rock, inadvertently stepping on an officer who was observing from a cleft.
The victorious army marches back into town, with Johnnie among those leading. He peels off and sits on the rear of his locomotive. When he goes into the cab, he finds the forgotten Yank officer just waking up. He escorts him to Division Headquarters and hands him over to the General. After a brief explanation, the General has Johnnie remove the uniform that does not belong to him, as Annabelle and her father watch. The General then gives him an officers coat and the Yankees surrendered sword. He poses for Annabelle and is enlisted as a Lieutenant.
Johnnie takes Annabelle to the General, and they sit together on the siderod. His kiss is interrupted by the need to salute a passing soldier . . . then another . . . and another. Then a whole regiment approaches, so Johnnie repositions so he can kiss Annabelle while he pumps his hand up and down in salute after salute.