Coop has to escort an ex-marshal and his wife who once shot Coop in the back to the wagon train. In addition he hires three men temporarily who hate the marshal but have more extreme plans for the man without Coop's knowledge.
Hide hunters, hunters who kill buffalo for their hides only, have temporarily joined up with the wagon train. One of their number, Gib Ryker, is a sociopath who enjoys antagonizing young Barnaby West. With the train desperately needing fresh meat, Cooper Smith, along with Barnaby, sets off with the hide hunters to look for buffalo. Along the way Gib continues to bait Barnaby, much to Coop's dismay until Barnaby is forced to defend himself, with disastrous results. Now Barnaby has to face Gib's brother Zach, who's out for revenge.
John Gillman being chased and shot in the leg by a posse escapes via a river. He is found downriver nearly passes out by a young orphan girl Abigail. She takes a liking to him but he tries to rebuff her. Wowever, events cause a change.
Bill accompanies Barnaby to Sam Race's tent city of "entertainers", where a girl from the train that Barnaby likes has taken a job, not as a singer, as she had thought, but as a saloon girl. Bill hopes to keep Barnaby out of trouble with the gambling and con games Race runs, but trouble and humiliation is just what they both find.
Cooper Smith is on his way to the town of Washburn to pick up long awaited mail for the wagon train when he stumbles upon a stagecoach robbery in progress. The very proper Miss Barbara Lindquist is on her way to meet her fiancé, mistakes Coop for one of the robbers and ends up forcing him to help her. Further misadventures see Coop wounded and both he and Barbara struggling to get to back to the wagon train for help. Believing his wound will end his days as a scout, Coop finds himself falling in love with Barbara and she with him. But will their love stand the test ...
Brian Conlin walks into Hale's camp, delirious and dehydrated. After he recovers, he leads Coop to his group of Irish immigrants, whose wagons have broken down, and Hale invites them to join the wagon train. However, having been repeatedly turned away from place after place, most members of Conlin's group are slow to trust anyone or accept help.
Coop falls for a young half-Indian woman wandering alone in the wilderness. He brings her to the wagon train, where Hale discovers she is a survivor of a tribe totally massacred ten years earlier. A sheriff says she has killed two people.
Hale is unable to take everybody on the next phase and has to turn down some of those applying. One is Ben Campbell, an ex-convict who is being hunted by his escaped former partner, who believes Ben turned him in to the law among others.
Spoiled Nancy Styles, claiming to be the daughter of the owner of the company that owns the wagon train, is determined to get to Denver by forcing her way onto it and then Hale makes it clear he plans to bypass the city due to early snow.
A blind man called Sangre has joined the wagon train along with his guide. He is actually Coop's boyhood blood brother Richard Bloodgood, and he openly states his plan to kill Coop. Coop gets very hostile and refuses to discuss it whenever Charlie or Barnaby ask the reason Richard wants to kill him, but they know it has to do with the death of a beautiful woman long ago.
With Hawks ill and Comanches threatening to attack, an Army troop meets up with the wagon train. The Indians appear to greatly outnumber the soldiers, so to give the train hope the troop's lieutenant falsely tells Hale and Coop that there is also a relief column headed their way. Complicating matters even more, a sergeant from the troop recognizes Clay Shelby, a young man on the wagon train traveling with his pregnant wife, as a deserter from back in the Civil War whom he blames for the death of his brother.
Charlie has finally found someone else who shares his dream of man being able to fly, henpecked inventor Hector Heatherton, who has been working on an idea for building a flying machine so Charlie volunteers to build a machine for Hector.
While out looking for water Coop and Charlie are stopped by a gang of five, including two women, who are on the run after robbing a bank and killing three lawmen. The leader of the gang shoots Charlie after tying him up, and they take Coop to lead them through a mountain pass to get to California.
Hale finds his old flame Chottsie Gubenheimer (played by John McIntire's real-life wife Jeanette Nolan) working in a gambling house and in an argument with the owner, so he asks her to come with him and join the wagon train. He comes to realize that he's getting more problems than he bargained for.
Wanda Snow has several times seen events before they have happened, causing several people on the wagon train to accuse her of being a witch. A medicine show peddler/magician gets the idea to use her in his act, but this creates friction between him and his devious partner.
Coop and Charlie ride into a small village for supplies finding it deserted. There is an Indian who stays hidden and later three men and a woman ride into town. They have been looking for the woman's father in a cave filled with bats.
The wagon train comes across old Jamison Hershey and Herman, his 3000 pound Belgian horse. The old man has made it safely through hostile Indian territory because the tribes are so in awe of his horse. Hershey and Herman are invited to ride with the train, though it becomes apparent that Herman is not able to travel very fast and may hold back the entire group.
Don Brooke is desperate for money for his pregnant wife Bonnie, who's condition is too delicate for the long trip without more medical care so he seeks a bank loan. When he sees an opportunity at the bank, it leads to tragedy.
Teacher Mary Lee McIntosh refuses to pay what she feels is an excessive fee to join the wagon train, so she decides instead to follow behind it in her wagon alone, and refuses help from Hale. But after her wagon overturns, things change.
Tough and headstrong female ferryboat captain Samantha Stewart is asked by her son Johnny and his bride to accompany them on the wagon train to California, where they will board a ship for a Pacific voyage. But actually, Johnny is not telling his proud mother that her doctor has told him that she must stay with a dry climate on land or she will die.
Despite the advice of some Coop decides to visit former girlfriend Eloise Blee, but finds Eloise gone, and instead winds up being talked into posing as her twin sister Betsy's missing husband and father of her baby daughter.
Barnaby is forced to shot and kill a boy his own age who took a woman and her daughters hostage. He is cleared of any wrongdoing but cannot shake the blood he feels is on his hands plus the judge wants him to inform the boy's mother.
A white renegade rides into the wagon train camp with an Indian girl tied to a rope and forced to walk without food or water. He says that he is bringing her back to the tribe where she will be tortured and killed for killing the chief's son. Hawks, in charge of a smaller group until Hale and Coop meet them with the rest of the train, decides to forcibly take the girl from her sadistic captor and keep her with his group, even knowing that this may lead to an attack from the chief's tribe.
Coop tells Bill the story of the Earp brothers and the Silver Lady, a woman who was encased in a coffin of sliver coins that melted around her after the stagecoach she was riding on and guarded by Morgan Earp had an accident and burned.
The series' final episode begins and ends with the two characters who stayed with it from beginning to end, as Charlie tells Hawks about his earlier days working for trading post operator Jarbo Pierce. Jarbo, once a wild, hard-drinking man, had become a minister, though he could still take on any man who tried to fight him. When his younger brother Adam arrived at the post Jarbo found himself at odds with him as Adam preferred the wilder ways of life and didn't understand Jarbo's concerns for the Indians he traded with, and began working with a man who wanted to use ...