In the late 1800s, John Murphy wanders into a wild mining town controlled by a local tycoon. Instant enmity is born, but the gritty Murphy joins a local miner and a homeless waif to work a gold claim and fight the tycoon's influence. Murphy's decision to stay is reinforced when the tycoon's heavies kill the parents of neighbor children over control of a gold strike. Together with the local school teacher, Murphy becomes temporary father to the children.
A handsome but ineffectual priest joins the school and provides comic opposition to Murphy and a pair of brothers in the orphanage, one of whom has a bed-wetting problem.
Murphy befriends an embittered black boy and teaches him a useful trade—wagon driving. But a wagon wreck causes the boy to lose the use of his hand, and Murphy must help him cope with living without the only task which ever made him feel worthwhile.
Father Parker mistakenly trades some of the stock for a fast, beautiful horse... that no one can ride. He'd hoped to race it in the territorial fair to win the $1000 purse, but he's injured while trying to break the animal. A little retarded girl at the school proves to be the only one who can tame it, and despite everyone's concern, she indeed rides the horse to victory. In the comic B-story, Rodman tries to indict the school for gambling and horse-playing, but it turns out Rodman's boss likes to play the ponies too ... and wins a bundle on the big race.
A mountain man deposits a young boy at the orphanage. The boy soon turns out to be a young girl, attracting the amorous attentions of young Ephram. When he feels rejected by her, Ephram runs away, is caught, and thrown into a work farm. Will and the girl get arrested in a failed attempt to help Ephram. break out.
Murphy and Eli must finally wade in to con the authorities into releasing the kids from the workhouse.
Falling on hard times again, the school is seduced by an offer of ""state aid"" by a local official. Mae accepts the aid, only to learn that by doing so she has unwittingly agreed to some'terrible conditions ... including the departure of Murphy and Moses and putting the children to work making leather goods. She's finally able to kick out the unscrupulous officials when she discovers them tampering with the money earned by the children's labor.
Comic episode in which the son of the original owner of Gold Hill Mine comes back to reclaim the school. Mae and Murphy are worried until they discover he's harmless, loveable... and a little bit nuts.
Claiming he's an orphan because his parents are dead, an old man joins the school to achieve a lifelong ambition... to learn to read and write. Comical conflict arises with Rodman and Tuttle, but the old man succeeds... and wins the heart of a ladyfriend.
When Will happens upon a large gold nugget, his drunk father shows up in town and kidnaps him, convinced the boys know where there's more. Will is locked in a dank root cellar and nearly starves when his father is injured without telling the boy's whereabouts. Murphy and his dog, Mine, manage to find and save the boy.
Moses discovers that music is the key to reaching a withdrawn blind girl. But the only way the school can afford a piano is by letting a local entrepreneur use the saloon building temporarily as a casino. Rodman seizes upon this to attempt to shut down the school ... but fails when he himself succumbs to the gambling bug.
A runaway Southern boy, formerly a bugler in the rebel army, comes to the school and has trouble accepting Moses' status there. Simultaneously, undesirables in the area are forming a local K.K.K. chapter. The boy becomes involved with them and the group tries to railroad Moses out of town. Murphy, the Marshall, and the boy's long-lost father join Moses in doing battle with them.
Amanda, a pretty accomplice to a bank robbery, is in a stage wreck near Gold Hill while escaping from her crime. She dons the habit of a nun who died in the wreck to avoid capture, but winds up having to go to the orphanage where the sister was expected. She grows attached to the children, and warm and comic moments ensue before she and Murphy drop pretenses in a touching conclusion.
When Rodman's unruly son is kicked out of boarding school, Rodman enrolls him at Gold Hill making him pose as an orphan in order to spy on the school, and he learns the secret of Murphy's disguise. Murphy, Will and Ephram take the boy on a camping trip to keep him from telling their secret to his father. During the trip the boy comes to feel loved by Murphy and the others, so he agrees to keep their secret to himself.
A wealthy widow with a railroad fortune comes to Gold Hill hoping to adopt a son to take over the family business. She's very taken with Will, who would rather stay with Murphy, but Murphy is torn between his love for the boy and the advantages of his adoption. The widow finally sees that the bond between Murphy and the boy is something she doesn't want to destroy and she withdraws her adoption bid in a complicated and interesting way.
The death of an abandoned child drives Father Parker to forsake the priesthood. He moves to Jackson where the only job he can find is cleaning out the saloon. In his secular adventures he finds himself protecting a boy and a pretty saloon singer from an unscrupulous gambler. The self-confidence he gains leads him back to his priestly role, with a little extra convincing from Murphy.
The orphanage stages an Open House for potential adopting parents, and this all-kid show examines the reactions of many of the children to finding new homes. Several of the kids find homes; our regulars are left behind until the next ""dream day.""
Lizette's heart is broken when Father Parker sells Laddie, an aging horse. When the kids learn the horse is bound for slaughter, Will leads them on an expedition to get her back, not realizing they're up against rustlers. Moses and Murphy race the clock to save the kids, the herd and Laddie.
Richard Garrett, the infamous twin of the villain from the pilot show, comes to Jackson to take over his late brother's empire. He doesn't reckon on resistance from Murphy when he tries to monopolize the town's freight lines nor on the fact that his young daughter will fall for one of the orphans, Matt.
When a teenage girl falls in love with Murphy, it forces him to examine his own feelings for Mae and he proposes marriage. At the same time, Father Parker's attempts to build a church in Jackson are thwarted by Garrett ... as a way of wreaking revenge on Murphy.
Emma feels rejected and in her upset state she divulges the secret of ""Father"" Murphy's identity to Rodman, causing the church to reverse its support for the new parish.
Mae and Murphy take a well deserved honeymoon in the city, where they meet young Eli Matthews, a streetwise black orphan. They swear they won't get involved, but naturally they end up adopting him and taking him back to Gold Hill.
A mother delivers her son to Gold Hill, saying that he's been incorrigible in school. The real reason is that his father is a child abuser and the mother fears for her son's life. When the father comes after the boy, Murphy intervenes and accidentally kills the man while trying to restrain him. Murphy faces the crisis he's feared all his life—that his great size and strength might kill if unleashed.
Sam Clemens (Mark Twain) arrives in Jackson during his itinerant journalist days, and sets up a newspaper to fight the evil influence of Garrett. Ephram and Will join him as copyboys/reporters, and in a comical turn of events, they become the inspiration for Tom Sawyer and Huck Finn.
Murphy and Mae join the Pinkertons on a cross-country train chase when one of their young orphans becomes heir to a large inheritance... and is kidnapped in an attempt to keep her from showing up to claim it.
Mae announces joyously that she's pregnant and the whole community rejoices... except Will. Finding out that the new bedroom Murphy is building is not for him, he feels ignored and finally, at the baby's birth, he runs away to St. Louis.
Will has run away to St. Louis and fallen in with a Fagin-type and his band of criminals. Murphy enlists Farley's help in searching for Will and goes to convince him to come home.
Lizette grows up; she begins work as an apprentice seamstress in town and falls in love with a n'er-do-well teenager. She's nearly drawn into his troublesome circle of friends before Mae shows her the error of her ways. The boy eventually reforms and then remain friends. Incidentally, the ongoing romance between Will and Lizette is terminated in this period because he is too short.
Murphy and Moses find trouble on a freight run when an old yarn-spinner convinces a whole town that Murphy is a famous bank robber. The fireworks begin when the real robber shows up.
Young Matt is witness to a bank robbery. One of the robbers is a teenaged friend of Matt's who is the sole support of a sick mother, and Matt must wrestle with his conscience as he decides whether or not to turn in his friend.
An ex-gunfighter gets out of prison and comes to Gold Hill to retrieve his son. He finds his son in love with his dad's old criminal image. Murphy and company must help these two come to an understanding and reconciliation.
A teenaged girl in town becomes pregnant, and after a suicide attempt fails, she's found by the Murphys and brought to Gold Hill. She learns a lesson in living, and the children learn a lesson in tolerance.
Garrett ruins Gold Hill's benefit Fourth of July show by stealing all the fireworks Murphy has especially ordered and locking them in his saloon safe. A comical old safecracker on the lam befriends Murphy and the kids and liberates the pyrotechnics ... in a most unusual way.
The kids decide Moses needs some romance in his life, so they send away for a mail-order bride. Her arrival precipitates comic explosions in Gold Hill, but by the time Moses realizes she's a wonderful woman, she's decided to go back to her old boyfriend back east.