Pat receives a telegram that Jack Barron, the leader of an outlaw gang comprised mostly of men who rode with Quantrill's Raiders during the Civil War, is heading to Lincoln to avenge himself upon Billy Bonney for killing one of his men when he tried to rustle some cattle. The townspeople fear that Barron's gang will raze the town if they don't turn Billy over to them, but Garrett deputizes the Kid instead.
Elena, Pat's former girlfriend, returns to Lincoln looking for protection. The man she left Pat for, Joe Durango, is an outlaw and a deadly gunfighter. She believes that the only place Durango won't look for her is in the town where her spurned lover is sheriff. Unfortunately, Elena underestimates Durango's ability to follow her footsteps. The gunfighter plans to exact his revenge on both Pat and Elena using the town's Fourth of July celebration to cover his gunplay.
While visiting El Paso on vacation, Pat Garrett finds himself in a high-stakes poker game and takes a young farmer to the cleaners. The man's wife convinces Pat to return his winnings because the young man can't pay his other debts. Only later does Pat discover that the farmer wasn't married and the pretty blonde was a clever con artist. With Billy's help, Pat tries to beat her at her own game.
Billy ignores Pat's warning about marauding Apaches and rides to Santa Fe to keep a meeting with a pretty girl. On the road, Billy is wounded by the Indians and takes refuge in an abandoned fort where he finds three women, one of them pregnant and several children. Billy must organize a defense when the Apaches regroup for another attack.
Billy introduces Pat to his current girlfriend and her father, Ben Wiley. Pat thinks he recognizes the man as the informer who ruined his attempt break out of a Confederate prisoner of war camp during the Civil War resulting in the death of one of Pat's men.
A scruffy no-account shows up in Lincoln with Mary Susan, his lovely teen-aged daughter, and tries to arrange her marriage to whichever bachelor will pay him the highest price. Pat Garrett and Billy Bonney intervene and runs the pair out of town. When her father becomes drunk, Mary Susan flees his campsite and returns to town set on marrying either Pat or Billy.
Pat arrests Archie Keough, a drifter who can't pay his bar bill. In jail, Billy recognizes the old man as his stepfather's best friend and Pat releases him under Billy Bonney's recognizance. Archie repays Billy's kindness by robbing a saloon, murdering the bartender and planting evidence that implicates Billy with the crimes.
Pat kills a man who was trying to steal a horse from the Lincoln livery stable. Billy recognizes the man as being one of a party of pioneers traveling across the Tundall ranch. When Garrett reports the death of the horse thief to the party's leader, Jeboriah Henry decrees that unless his widow shows mercy, the sheriff will die for killing her husband.
Billy Bonney quits his job at Tundall's ranch and at the urging of his new friend Swade Hiney, plans to join an outfit run by Jake Newton. Billy learns that Newton is nothing but a cattle rustler, but can't get away before the local sheriff and his posse arrest Bonney, Swade and Newton. The ranchers whose cattle Newton has been stealing organize a lynch mob to kill the men before Pat Garrett can come to Billy's aid.
Billy falls for a beautiful girl who doesn't believe in guns so, to impress her, he gives his holster and derringers to Pat Garrett so he won't be tempted to use them. This provides Bart Conway with a golden opportunity to steal Tundall's ranch and he orders two of his men to kill Bonney while he is unarmed.
Pretty suffragette Amy Dodds throws a brick through a window in the Lincoln County jail. When Pat Garrett refuses to arrest her, she marches into Murphy's saloon and destroys his beautiful bar mirror and most of his liquor bottles with a barrage of bricks. When Garrett finally arrests her, she tells a newspaper reporter that the sheriff mistreated her in prison to gain publicity for her cause.
Trying to stay out of trouble, Billy accepts a new job as a shotgun guard for a stagecoach line. What seemed like a peaceful job quickly turns violent when his stagecoach is held up by two outlaws resulting in a murdered driver and a stolen strongbox. Billy guns down one crook and manages to recover the money, but buries the loot in hopes of luring the other criminal out of hiding.
Upon learning that a New York reporter has traveled West to write about a series of articles about "The Bad Men of the West", Billy spins wild tales of his criminal exploits. When the newspaperman wildly expands about Billy's yarns, the New Mexican government orders an investigation into Sheriff Pat Garrett career as a lawman.
A block of marble meant for a Lincoln businessman's tombstone is stolen from a stone cutter's shop and Garrett suspects Billy Bonney of the theft, though he can't prove it because he can't find the slab. Billy took the tombstone for the most honorable of reasons - to mark the grave of a pulper's widow.
Billy thrashes Sledge when the brutal wagon driver tries to lash a young Mexican boy with a bullwhip. When Garrett learns that sledge "purchased" the boy from his impoverished parents for a few dollars, he kicks Sledge out of town and instructs Billy to escort the boy back to his village. Bonney learns that Sledge works for a owner of the town's trading post and the crooked businessman has all of its citizens in his thrall because of his shady practices.
Garrett negotiates the return of a girl, now a full-grown woman, who was captured by the Apaches nine years earlier. Although her father welcomes her back with open arms, the former captive yearns to return to her husband, Talano, a noted Chirachaua warrior, who has sworn to kill any white man that tries to prevent her return to his village.
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.