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In the early months of the Civil War, Confederate guerrillas led by the notorious raider Wade McQuarrie move into the western territories, wrecking havoc and looting in the name of the South and General Lee. At the same time, at the Union's Fort Aldrich outpost, townspeople suspect Dr. Seddon of Rebel sympathies and prepare to hang him. Military scout Gene Autry intervenes, and during the subsequent brawl, news arrives via the Pony Express that the Federal forces have suffered a major setback. The townsmen, including Gene, rush to enlist, but fort commander Maj. Weatherly asks Gene to delay his enlistment and continue scouting for the Army to locate the wily McQuarrie. Gene agrees to the dismay of his best friend, Pat Claggett, who has also enlisted. Pat nevertheless accompanies Gene on his search, and soon after, outside the town of Gateway, the pair comes across an Army wagon whose escort has been killed and a safe filled with silver destined for Washington, D.C. stolen. The wounded driver manages to reveal that McQuarrie and his men were the assailants. While Pat tends to the wounded soldier, Gene rides into the hills, where he comes across a mule train led by Laughing Jack, who claims he saw nothing of McQuarrie or his gang. Farther down the trail, Walt Middler, a Confederate sympathizer and head of the local stage line, tries to pick up McQuarrie's tracks. When his sister Dell rides up, Walt takes her fresh horse and abandons his lame mount. Gene discovers Dell and despite her hostility, takes her into Gateway, where she quickly darts away. Pat rides into town while Gene consults with Walt and Dell's father, Col. Middler, the desk-bound head of the area's Federal troops. Gene presents himself as a horse trader, a claim that both Walt and Dell regard with suspicion. When Gene and Pat hear a report about the theft of several horses, they ride out to investigate. At the small Pony Express station, they are driven off by McQuarrie and his men, who steal the mail and discover a newspaper report that General Lee has denounced McQuarrie and ordered his guerrilla outfit to disband. Back at his cave headquarters, McQuarrie announces his intention to go on fighting with his most daring raid yet. In town, Walt continues to be suspicious of Gene, while Dell worries about her brother's possible involvement with the guerrilla attacks. A few days later, McQuarrie, in a captured Federal uniform, reports to Col. Middler under the name of Capt. Fleming. Meanwhile, Gene and Pat examine McQuarrie's men's horses and discover they bear the brand of the recently stolen herd. When Gene tries to tell Middler, McQuarrie declares that Gene and Pat sold them the horses and therefore must be the thieves. Gene insists that he came from Fort Aldrich, but when Middler presents Seddon, the doctor states that Gene and Pat are wanted there as deserters. Middler has Gene and Pat arrested even as Gene demands that the colonel check on the captain. Later, Seddon sneaks to the back of the jail and gives Gene a gun, claiming that had he not spoken against, him he would have been murdered. Before he can identify McQuarrie, however, the doctor is shot in the back by one of the guerrillas. Gene and Pat break out of jail just as Middler gives Walt a note to telegraph inquiries about Capt. Fleming. Walt, however, does not deliver the message. Dell hides Gene and Pat and misleads McQuarrie and his men, who are searching for them, and then provides them with horses. Gene and Pat meet Dell at the telegraph post, but as they try to send a request to headquarters, McQuarrie and his men pull down the wires a mile away. The telegraph operator, however, recognizes that the military unit given by McQuarrie does not exist, confirming Gene's suspicion that Fleming is McQuarrie. Hoping to get to the next town to summon help, Dell stops the eastbound stage only to discover McQuarrie's cohort, Laughing Jack, inside. Jack forces Gene and Dell aboard, but Gene overpowers him and takes over the stage. Back in Gateway, McQuarrie, realizing that Gene is probably going for assistance, murders Middler, then he and his men pillage the town, killing several townspeople. Walt, outraged that the stage office was also vandalized, is dismissed by McQuarrie, who then departs with his men. Walt discovers his father's body, and when Gene and Army reinforcements arrive, offers to show them to McQuarrie's mountain hideout. Outside McQuarrie's cave, an intense shootout ensues, as Walt sneaks to a back entrance, determined to take revenge on McQuarrie. The guerrillas barricade themselves inside the cave as Walt slips in by the back and lights a fuse to the large supply of gunpowder. A wounded guerrilla knocks out Walt and tries to put out the fuse, but before he can warn the others, the powder ignites, burying McQuarrie, his men and the silver. Later, Gene and Pat return to Fort Aldrich to enlist in the Union Army.