At a remote ranch in the desert of New Mexico, homesteader Angie Lowe (Angie Lowe) and her six year-old son Johnny (Lee Aaker) come upon a stranger (John Wayne) drinking water from their river, carrying only a saddle and a rifle. The man tells them only his last name, Lane, and that he is part Apache and was exploring Indian Territory as a US Army Cavalry scout. His horse was stolen a few days earlier, and offers US Army scrip in exchange for one of her horses. Angie tells Lane that her ranch hand had quit recently and hadn't had a chance to break one of her two horses for riding, so Lane offers to break the horse himself. He also asks where her husband is, and she says he is hunting in the mountains and should be back soon. Johnny watches with fascination as Lane takes one of the horses, and saddles and rides the bucking and untamed animal with ease.
Lane also offers to do a few chores around the ranch, including sharpening an axe blade and chopping firewood. Lane deduces by the neglected work around the ranch that her husband has not been at the ranch for some time, a fact she is forced to admit. When night falls and the weather grows inclement, Angie offers to put Lane up in her home on a floor bed in the corner. Angie discovers that the butt of his rifle is inscribed to "Hondo" Lane, a name she knows to belong to a criminal, and she pulls a pistol on him and fires, but there is no cartridge in the first chamber.
She had left it empty so that Johnny wouldn't shoot it accidentally. Hondo returns to his Cavalry post, leaving Angie and Johnny alone at the ranch, where he meets up with his scout sidekick Buffalo Baker (Ward Bond) and reports to his commanding officer that the Chiricauhua Apache lodges in the area are banding together and attacking settlers. At the ranch, Angie and Johnny are surrounded by menacing Apaches led by Chief Vittorio (Michael Pate) and his sub-chief, Silva (Rodolfo Acosta). Angie is not nervous as she has always let them water their horses at her ranch and they had never hurt her. On this occasion, they threaten and grab Angie. Johnny emerges from the house with the loaded pistol and shoots at Silva, hitting and breaking his weapon. Vittorio is impressed by Johnny's bravery, and makes him an Apache blood brother by cutting Johhny's thumb with a knife and giving him an Apache name.
Vittorio wonders where Angie's husband is, and she tells him that he will return soon. Vittorio tells her that the boy needs a father to guide him, and unless her husband returns soon, she must take an Apache husband. A night or two later in a saloon, Hondo calls a friend from his poker game, but one of the poker party objects. He and Hondo get into a fight, and Hondo beats the man up badly, driving him out the door.
Buffalo Baker tells Hondo the man called himself "Ed Lowe" (Leo Gordon), and Hondo suspects he might be Angie's missing husband. Feeling guilty, he leaves the fort to return Angie's horse back to her. Seeking revenge for the bar beating, Lowe and an accomplice follow Hondo through the desert as he makes his way back to Angie's ranch. Hondo camps near a river but leaves it when he detects three Indians stalking him nearby. Lowe enters the camp and he and his friend are attacked by two Indians. The friend is killed, but Hondo shoots and kills an Apache about to kill Lowe. Lowe is briefly grateful but turns his gun on Hondo in retaliation for the bar beating. Hondo defends himself, killing Lowe.
Hondo finds a photo of Johnny alongside Lowe's body, confirming that Lowe is Johnny's father and Angie's husband. Continuing towards Lowe's ranch, Hondo runs into an Apache party, who pursue Hondo through the desert. He kills several but they eventually capture him. They take Hondo to the top of a nearby mesa when Vittorio appears. They stake him out and begin to torture and prepare to kill him because he is an Army scout. An Indian shows Vittorio the picture of Johnny from Hondo's saddlebag, and Vittoria thinks Hondo is Angie's husband. He orders the Indians to untie him and declares that he must fight Silva for honor, as he is one of Angie's potential suitors.
Hondo and Silva fight using knives. Silva wounds Hondo in the shoulder, but Hondo pins Silva to the ground. Hondo puts his knife to Silva's throat, but Vittoria steps forward and Hondo spares Silva's life, temporarily buying his own life in return. Vittorio takes Hondo to Angie's ranch, and when Vittoria asks if Hondo is her husband, she lies, saving Hondo.
The Chief warns Hondo to raise Johnny in the Apache way and leaves them. While Hondo recuperates from his wounds, he shows her the picture of Johnny that he tells her he took from Lowe's body. She asks if he died well, and Hondo pauses before saying that he had. Over the next few weeks, Hondo and Angie grow closer. Hondo and Angie express their growing love for each other. Hondo attempts to reveal the truth of her husband's death, but is interrupted by Vittorio's sudden appearance. Vittorio tells them that the pony soldiers will soon return.
He asks Hondo not to join them and to keep the Indian's location a secret. Hondo promises to do the first but not the latter, and Vittoria shows respect for Hondo's truthfulness. Angie tells him she loves him, and they cement their relationship with a kiss. The Army arrives at the ranch, commanded by an ambitious, inexperienced young Lt.
McKay (Tom Irish) and accompanied by scouts Baker and Lennie (James Arness). McKay is determined to take all the settlers in the area back to the Army post to protect them and defend the territory against Apache attacks. Lennie reveals that he discovered Lowe's body and matched the horse tracks to Hondo's horse. He wants Hondo's Winchester rifle in exchange for keeping quiet about how Hondo bushwhacked Lowe.
Angie overhears Lennie's demands. Hondo prepares to leave, but before he goes, he tells her the truth about her husband's death. Hondo is also intent on telling Johnny, but she persuades him not to, telling Hondo she didn't love her husband any longer and had grown tired of his womanizing and gambling. She says it would be an unkind thing to tell the boy about the true nature of his father's death and that the secret won't follow them to Hondo's ranch in California. Hondo responds to her emotional plea with an Indian word that seals a squaw-seeking ceremony, "Varlabania", which he tells her means "forever". The Army leaves to move further on into Apache territory and as promised Hondo refuses to go with them but tells them where Vittorio and his party are. The Army returns after being ambushed by the Apaches, suffering heavy casualties including wounds to Lt.
McKay. Vittorio had been killed, causing the Apaches to retreat so they can regroup and select a new chief. Hondo leads the Cavalry and settlers back towards the fort, taking Angie and Johnny with them. The group is attacked by the Apaches, now led by Silva, but the group circles their wagons. They escape the encirclement twice but the Apaches continue their pursuit.
Hondo loses his mount and is attacked by Silva, but Honda kills him, retrieving Lt. McKay's uniform shirt from his body. The Indians retreat again to choose a replacement chief. Lt.
McKay says the General Crook will be arriving in the territory with a large force to pursue the Apache. Hondo sadly notes the end of the Apache "way of life. ".