The McBeans receive word that the railroad will be laying track across their hardscrabble ranch and, as a result they will be evicted. May and June hatch a wild scheme to lure Pat Garrett away from Lincoln so Pa McBean can pose as the county sheriff and intercept the process server before he can legally remove them from their land.
Billy is framed for murder by his old nemesis, Bob Tollinger, who is now the sheriff of a neighboring county. Joining him on the trip to his date with the gallows is a pretty female prisoner, Anne Drake, also falsely convicted of murder. Billy and Annie manage to escape, but must flee the pursuing posse while manacled to one another.
A widow who is engaged to Tom Davis, a friend of Pat's, arrives in Lincoln with her young son. Davis asks Pat to look after his fiancée until he can return from a cattle drive and the widow begins to wonder if Garrett might be a more suitable husband than the man she is pledged to marry.
A wealthy young man arrives in Lincoln seeking a guide for his hunting expedition. He convinces Billy Bonney to lead him into the wilderness in order to bag a mountain lion for his collection. Once in the wilderness he informs his guide that his real quarry is Billy himself.
Lincoln population swells when an Apache uprising closes the roads leading out of town. With the town's hotel and boarding house filled beyond their capacities, the civic-minded Garrett agrees to allow his jail cells to be used temporarily by stagecoach passengers who trapped by the Indians' depredations. Pat soon regrets his actions when the passengers turn out to be mail-order brides impatient to meet their new husbands.
Garrett is traveling through Mexico with a prisoner bound for trial in Lincoln. An impending storm forces the pair to take shelter in a small poverty-stricken pueblo where the seemingly friendly villagers offer to them hospitality. It soon becomes apparent that the townspeople expect to be well-compensated for their help.
While trying to ride a bucking bronco, Billy is thrown violently off the horse's back and smashes his head against a wooden post. Taken to Lincoln for medical examination, the doctor decides that Billy has a concussion and prescribes medicine to keep him unconscious for at least twelve hours. The medication has the opposite effect on Billy - worse, he barricades himself in the cantina, believing everyone in town is conspiring to hang him.
A young Mexican woman arrives in Pat Garrett's office with a centuries old document that appears to be a Spanish land grant which gives her family title to half the land in Lincoln County. Garrett can't believe that the document is the genuine article, but after consulting with experts in the territorial capital in Santa Fe is forced to concede it's legitimacy and makes plans to evict the county's erstwhile property owners.
Garrett is ordered by Governor Lew Wallace to provide every assistance to a small cavalry patrol attempting to negotiate the surrender of a renegade band of Apaches. Neither Pat nor Billy Bonney, who has been hired as a scout, believe that the officer leading the patrol, a stern martinet, is the man for the job.
Garrett arrests the Killgor brothers, a pair of brutish drifters, for busting up one of Lincoln's saloons. Pat doesn't pay attention to the drifters' threats about their mother's viciousness, but the woman pistol whips Pat and frees her brood, locking Pat in their cell. The Killgores then steal sheriff's badges and embark on a crime spree.
Garrett interrupts a gang of bank robbers who were attempting to break into the bank's safe and is forced to shoot one of the three thieves. While the outlaw is having his wounds tended to, a man staggers into the doctor's office suffering from symptoms of the bubonic plague. For the town's safety, the physician asks Garrett and the outlaw to remain in his home under quarantine.
Jacques Montreaux, a showman with four beautiful performers arrives to perform at the local opera house. He reports to Garrett that in a dressing room at another theater, he found a letter from a woman begging her daughter not to carry through her plan to murder Billy Bonney. Billy laughs the threat off as a joke, but Garrett investigates and discovers that all of the women in the troupe have something to hide.
Billy hops a freight train when his horse dies far from civilization. Unfortunately, it's the same train on which a federal marshal investigating the shipment of contraband rifle is found murdered. Billy is framed for the crime by a crooked sheriff who is involved in shipping illegal liquor throughout the Southwest.
A meek middle-aged man walks into Garrett's office and demands to be arrested for robbery and provides a carpetbag full of money as evidence. He tells Garrett that he stole the money from a crooked politician in St. Louis and agrees to testify against him if the lawman will protect him on the return to Missouri since he's convinced that gunmen have been hired to kill him. The sheriff is reluctant to believe his prisoner's wild tale until he receives a telegram collaborating the theft and a notorious killer for hire appears on the streets of Lincoln.
Billy receives a letter from an old prospector whom he staked to a month's digging money stating he might have found a lost Spanish mine near San Miguel, a ghost town in southern New Mexico. Along the way he meets two other investors who received an identical letter. Instead of finding an old friend, the trio meet a judge bent on correcting the supposed errors of juries that found the three defendants innocent in murder trials the jurist presided over. Convinced of their guilt, the judge demands a reckoning.
Isobel Stewart, an old flame of Pat's, stops in Lincoln with her husband, Henry, who is dying of a rare disease. Unbalanced after receiving a medical opinion that his illness is fatal and jealous about Pat's friendship with his wife, Stewart plots to commit suicide, while trying to frame his death to make it appear that his wife murdered him.
The Tugwell brothers and their pretty sister, Sally, come to Lincoln to find Sally's husband who left her immediately after getting married a year earlier. Sally has an infant baby and her brothers insist that Pat help them find Sally's ne'er-do-well husband - William Bonney aka Billy the Kid so he can make an honest woman of their sister. Billy, though, insists that he's never seen the young woman in his life.
Concerned about the prospect of an Indian war with the Mescallero Apaches, Governor Lew Wallace asks Pat to investigate reports that a French foreign agent may be providing guns to the Apaches. The United States government fears that a European power may be stirring up trouble as a diversion to hide their true objective - the reoccupation of Mexico.
Don Diego, a wealthy Mexican-American landowner, and Rosa, his beautiful fiancée, have a falling out which ends in angry words and mutual recriminations. Rosa places a curse on Don Diego and his family and his son immediately dies from a horseback accident. Don Diego demands that Sheriff Garrett arrest Rosa for witchcraft.
A young doctor arrives in town to take over the practice of a beloved physician who recently died. Although his skills are marvelous and his knowledge prodigious, his poor bedside manner quickly alienates the townsfolk who he was hired to treat. His future rests on his ability to save a pregnant young woman who tried to commit suicide when she was deserted by her husband.
When a vengeful father sees Billy Bonney with a necklace that belonged to his runaway daughter, he accuses the gunslinger of murdering the teenager. Billy had received the jewelry as a gift from the young woman for treating her wounds when she was injured in a rockslide, but now he must find the girl to prove himself innocent. If he does find the girl, her father plans to beat her within an inch of her life for being disobedient.