Clay Stafford signs on to work for the Cartwrights and shortly afterwards shoots and kills a man who accuses him of cheating at poker. The miners warn Clay to leave town, but it appears he killed in self-defense. Surprisingly, he tells Little Joe that he is his half-brother, and Marie was his mother. Ben listens to his story and takes his word for it, but Adam and Hoss think he should wire the judge in New Orleans to confirm Clay's real identity. Meanwhile, Clay and Joe develop a close relationship, but the vengeful miners still want Clay out of Virginia City and their first warning, is when Joe is beaten up by them. Ultimately, Clay decides life on the ranch is not for him.

Determined to prove he can succeed at something without the help of his Pa, Hoss, and Adam, Joe sets out on his quest and wins a timber contract for Ponderosa timber, and later discovers that having a family to rely on can definitely be an asset.

Ben helps Matthew Raine, a famous painter who has gone blind and now wallows in self-pity, discover a new purpose in life. However, Raine's employee Gavin has other ideas.

Hoss is jailed for robbing the bank in Dutchman Flats, a town on the brink of economic collapse, even the sheriff knows he is innocent, but a lynch mob gathers and Hoss' fate is not good.

An Indian-hating officer, Colonel Edward J. Dunwoody, comes to the Ponderosa looking for army deserter Bill Winters, who is a good friend of the Cartwrights. Bill happens to be his son and is married to an Indian. It seemed Bill deserted when he was ordered to massacre the Shoshone, by poisoning their food and water, genocide. The Shoshone find out and abduct Bill's father.

With a storm brewing, Adam takes refuge at a way station, run by cantankerous Jesse and his young grandaughter Marty, who yearns to see what exists away from the way station. The station is also visited by Luke Martin, a killer who is running from a posse. He makes Marty an empty promise to take her with him and see the world together, but Adam steps in and suggests Luke let her alone. Everybody but Marty is relieved to see him go, but he quickly returns and holds everyone hostage to protect himself from the posse.

The Civil War once again divides the citizens of Nevada, as well as Adam and Joe Cartwright. One of season four's highlights, the plot involving British spy Bill Stewart, based on historical fact.

Hoss volunteers to pickup an injured neighbor's mail-order bride, but by the time they return, she has fallen in love with Hoss and a price is put on Hoss' head.

Billy Horne is a white man who was captured by the Shoshone when he was six. He comes into Ben & Joe's campsite one night uninvited. They capture him and take him to town. Roy Coffee wants to put him in jail for safekeeping, but Ben says he'll take him to the Ponderosa. They buy Horne clothes and become friends to him. A guy named Milton Tanner says the deed to the Ponderosa is weak and tries to take a third of it. Billy goes to Tanner's ranch and warns him that he will kill him if he tries to take the land. Tanner turns his dog loose on Billy. Billy kills the dog and then Tanner, who is going for a gun. Billy pleads guilty, but breaks out. Eventually he goes back with Joe and tells what really happened.

The Ponderosa becomes a war zone when it is invaded by a detachment of Mexican mercenaries under General Diaz. The general is furious when one of his men, Forsythe, disobeys his orders to get a hostage peacefully, and instead shoots Little Joe in the back. Diaz forces Ben to lead his men over the back roads of the Ponderosa, so they can ambush a gold train led by Emperor Maximilian's men.

Hoss helps Charlie and Will (Charlotte and Willomina), two young girls who just lost their father. They go on a journey to find their only nearby relative, Aunt Cloe. Charlie takes with her a stolen sack of money that her father gave her and tries her best to lose Hoss. Four bandits show up looking for the loot Charlie has. In the end, Hoss finds out about the stolen money and talks the girls into giving it back. He puts them in dresses and sends them off to Boston on a stage, telling them they did the right thing and will probably get the money back as a reward for helping capture the bandits!

Hoss is seriously injured internally and Ben seeks help from the only doctor within 50 miles, who happens to be in prison for murder. Ben talks to the judge, and with some convincing, talks him into letting the doctor look at Hoss. Danny, who works for the Doctor, tells Ben what he saw about the murder. Ben discovers what really happened and proves to the judge that the doctor really is innocent. The judge stops the hanging and Hoss survives.

Hoss decides to help out Wade Tyree and introduces him to Abigail and her daughter, Bonnie. Hoss hopes this will stop Wade's constant drinking. Wade soon marries Abigail, but when things don't go his way, he goes back to drinking. Hoss helps out by helping the new family plant crops. When no rain comes, Hoss introduces them to irrigation, and Abigail faints while watering the crops. Wade realizes he has been a terrible husband and father, but gets a second chance when Abigail finds out she is going to have another child. Abigail and Bonnie both forgive Wade and a new family is born!

When Hoss is responsible for causing a hung jury, Ben tells him, "a man is never wrong doing what he thinks is right", and Adam attempts to validate his brother's reasonable doubt.

Frank Medford, a figure from Ben's "wild, misspent youth", shows up in Virginia City, and though down on his luck, creates troubles for the Cartwrights by claiming to be a successful businessman.

Adam's guitar-strumming friend, ranch hand Danny Morgan, is arrested on suspicion of murdering and robbing the Widow Baker. Someone had reported hearing Danny singing outside her place at the time of the murder. More, importantly, Morgan has bad scratches on his arm, and the widow was found with human skin under her fingernails. Adam is thoroughly convinced that Danny couldn't have done it; the two became friends after Danny saved Adam's life a few years ago.

A stranger, Bob Jolly, arrives in Virginia City to accuse a drunken Judge Harry Whitaker of sending his innocent father, Carl, to the gallows. Adam defends the judge's honor because of his long friendship with the Cartwrights. After Adam talks with Jolly, he begins to believe his story. Upon further investigation, Adam discovers that Senator Cal Prince and Hobie Klinderman as well as the judge might have had a lot to gain from Carl Jolly's murder. In an attempt to learn what really happened, Adam organizes an informal meeting in the saloon.

In this entertaining episode, laced with humor, Hoss first meets mountain man Jim Leyton. Bing Russell makes his first appearance as Deputy Clem Foster.

A vain outlaw murders a man in front of witnesses, including Joe, but a clever lawyer is able to get him acquitted. Though enraged, Joe has to convince the dead man's son it is wrong to take the law into their own hands.

When Cochise falls on Joe, Ben cannot help but remember that is how Marie Cartwright was killed. He thinks back to meeting her in New Orleans in a rather confusing story not quite in synch with details discussed in "The First Born".

For a change, it is Adam rather than Joe who becomes mixed up in one of Hoss' funny exploits. Together they purchase a thoroughbred horse, and end up competing against their little brother in the big Virginia City race. This is Pernell Robert's favorite comedy episode.

Joe becomes romantically involved with a woman who considers herself a serious dramatic actress. Unfortunately, she is the only one who does.

Hoss develops amnesia after being bushwhacked and hit over the head by two outlaws and moves in with a Dutch couple. The woman regards him as a substitute for her dead son, and unless he recovers his memory, the other Cartwrights fear he will leave them forever.

Adam takes a shine to Rebecca Kaufman, the daughter of a Jewish peddler, and bandits are convinced the Kaufman wagon is worth robbing.

Ben's attempt to rehabilitate an alcoholic singer he knew in better days are complicated by her involvment with a former prize fighter.