It's 1885 in Arizona and an Army Captain has dispersed his troops to keep the whites off of Government land thereby keeping the peace with the Apaches. But there are those in Tucson that want the miners back looking for gold and they put pressure on officials in Washington. Soon a new commander arrives, the troops are recalled, and the miners go after gold. Whites then kill a miner with an arrow so they can attack the Indians hoping the troops wipe them out when they retaliate.
Captain Hunt of the cavalry is trying to promote good relations with the Indian chief Acoma. But Hunt's superiors in the military insist on pursuing policies that will provoke a conflict, and Chief Acoma is not willing to let himself be insulted.
A cattle baron takes in an orphaned boy and raises him, causing his own son to resent the boy. As they get older the resentment festers into hatred, and eventually the real son frames his stepbrother for fathering an illegitimate child that is actually his, seeing it as an opportunity to get his half-brother out of the way so he can have his father's empire all to himself.
Gene Autry hunts bank robbers Al Bartlett and Trot Lucas with his old friend Mike. Bartlett, to throw off his pursuers, kills Trot and his own brother. When Kitty Bartlett comes to town claiming to be the slain Bartlett's widow, Gene has to save her from the irate townspeople who are not aware that her name isn't Bartlett but she really is the daughter of a law officer slain by Al Bartlett. Ben Luder, a local hood, tricks Bartlett back into town by saying he has to fixed to have Doc Larry Taylor do plastic surgery on him. En route they meet Doc and his assistant Helen Ellis and Ben's ruse is exposed. Bartlett kills Ben and forces Doc to drive him to the railroad. Gene, in a fight atop a runaway train, captures Bartlett.
Lt. Col. Kirby Yorke is posted on the Texas frontier to defend settlers against depredations of marauding Apaches. Col. Yorke is under considerable stress by a serious shortage of troops of his command. Tension is added when Yorke's son (whom he hasn't seen in fifteen years), Trooper Jeff Yorke, is one of 18 recruits sent to the regiment.
When asked about the Ghost Riders song he sings, Gene Autry tells this legend: Gene is about to resign as an investigator for the county attorney and go into the cattle business with his pal Chuckawalla Jones but decides instead to help Anne Lawson clear her father, rancher Ralph Lawson, of a false murder charge. He looks for the three witnesses who can testify that Lawson shot only in self defense in killing a gambler, but the witnesses are terrorized by another gambler, town boss Rock McCleary, who shoots witness Pop Roberts Morgan. Fatally wounded, Pop gives Gene the information needed to clear Lawson, then dies crying the "Ghost Riders" are coming for him. Gene then heads for a showdown with McCleary.
A prospector is looking for a lost gold mine and finds aid in his search through the efforts of his friend, Stormcloud, whom he has aided in the past. Stormcloud gives the prospector's son a map leading to the mine in repayment for his past kindness. When a claim jumper learns about the map, he targets the prospector and his son in order to get the treasure.
Finding Indians stealing from his ranch, Gene learns they are suffering from malnutrition. Store owner Martin is cheating them and now he is after the Chief's valuable necklace. When the dying chief is found, having been attacked and robbed, Martin blames Lakhona who would become the new chief. When Gene helps Lakhona they soon find themselves fleeing from the law.
Saloon-bar singer Freddie gets very angry whenever boyfriend Blackie seems to be playing around. She always packs a six-shooter, so this is bad news for anything that happens to be in the way. As this is usually the local judge's rear-end, Freddie and friend Conchita are soon hiding out teaching school in the middle of nowhere.
While trailing Forest Ranger Charles Carter, who is suspected of permitting lumber man Henry Mitchell to cut restricted timber, Gene fires at a dangerous mountain lion and apparently kills Carter. Actually, Bill Wright, Mitchell's associate, killed Carter because the ranger had discovered tussock moth infestation in the forest, and if the infestation was not reported, the trees would die and have to be cut, thereby profiting Mitchell and Wright. In order to compensate the best he can, Gene sells his sportsman's camp and gives the money to Carter's daughter Helen . En route to Texas, Gene discovers the infestation and is assigned by the Forest Department to supervise the program of spraying the area with DDT from the air. After the first day of spraying, the DDT is blamed by furious stock men for the many animals found dead of poisoning.