Hoss and Little Joe are mistaken for bloodthirsty hired killers in a small Texas town dominated by two feuding families.

The Cartwrights come to the aid of a Chinese-American stable hand accused of murder. Opposing them is a manipulative mayoral candidate who wants all "foreigners" to leave Virginia City.

The Cartwrights try to disprove the validity of a Spanish land grant to stop the De La Cuesta family from seizing part of the Ponderosa and all of the Carson Valley settlers' homestead lands.

Jeb Drummond is a murderous sheep herder that has Adam taken hostage to try and force Ben to sign over a large section of Ponderosa land to him.

As is often the case on Bonanza, things are not always as they first seem. Hoss and Adam eventually learn who is the good guy and who is not.

Inspector Leduque comes from New Orleans to Virginia City to take Ben Cartwright back for a 20-year-old murder. When Ben declares publicly that he is withdrawing from the Governor's race, the townsfolk are upset not just about this but Little Joe has also been accused of gunning down Leduque's deputy in cold blood.

Three deserters escaped from an Army stockade to the Ponderosa. When a Captain comes looking for them, Ben realizes what they've had to deal with and promises to let his good friend in charge of that fort know the real truth.

Ben and Adam are locked in jail, about to hung for a crime they didn't commit. Joe and Hoss must find out why the witnesses to the alleged crime have perjured themselves before the execution takes place. They receive help from an unexpected source, a drifter called Lassiter who is searching for the men who committed a lynching in Kansas years ago.

While in San Francisco, two of Ben's hired hands get shanghaied and so does Ben in the process of looking for them.

A neighboring rancher, Andy, is good friends with Ben, but his son (Todd) wants to sell their land for mining operations which will spoil the water rights agreement that Andy and Ben made years ago.

A woman dies. Her husband is in prison, and the sheriff needs someone to look after the boy until the boy's uncle can come to claim him. The Cartwrights begin to take care of the boy at the Ponderosa. When the boy arrives at the ranch, he does not know that his father is in prison. The boy learns the truth about his dad, and news reaches the Ponderosa that the convict has escaped from prison. The Cartwrights deal with the possibility that the boy's father may be coming their way.

While hunting a predator wolf, Little Joe finds a gypsy woman who has been rejected from her people because she is believed to be a witch.

When a powerful gang plagues Virginia City with a murderous protection racket, the Cartwrights are determined to stop it even as it threatens them.

An outlaw gang robs Virginia City's bank and makes off with almost all of its money. The youngest member of the gang manages to get a job on the Ponderosa as a bronc-buster with the intention of informing the bank robbers of any posses that may threaten their hideout. While Ben, Adam and Hoss welcome the newcomer, Little Joe becomes suspicious of his activities.

Charlie Trent used to be an Army scout. Now he's the town drunk. Hoss helps him regain his self-esteem when he has him volunteer to lead a gold-bearing troop through the desert where there's very little water.

After a U.S. deputy marshal apparently saves Adam's life by gunning down two men who shot at him, he eventually reveals that he's in town to bring a close friend of the Cartwrights to Sacramento to testify in a statewide racketeering trial, but the deputy marshal's motives soon become suspect as to what he really wants to do with the reluctant witness.

The Cartwrights' neighbor Tom Edwards has lived as a paraplegic, ever since an accident involving Ben Cartwright and a gun. His ranch is going to waste. His wife Joyce is a longtime friend of Ben, and Ben decides to help the Edwards couple by making Tom a business proposition: the Cartwrights will build a grain mill on Edwards' land. In return, Ben only wants his investment money back, plus fifteen percent. Tom and his hired hand Ezekiel are suspicious of Ben, but Tom agrees to the deal. The Cartwright men build the mill, but tension begins to rise when Ezekiel makes comments which rekindle Tom's suspicion.

Jacob Darien is leading his family of Quakers through Virginia City. When he is accosted by town roughnecks, Adam Cartwright steps in with the help of his new traveling companion, Sam Bord. Adam offers to escort the wagon train across the Ponderosa, unaware that Sam is planning a robbery.

Ranchers are being killed, cattle stolen, and even after former U.S. Deputy Marshal Denver McKee sends posses after the suspects, they are never found. Meanwhile, McKee suspiciously has plenty of money to take care of his daughter and her schooling back East.

Prejudice erupts on both sides when Ben gives an Indian named Matsou and his wife some of his land, after saving Ben's life from a renegade Indian who almost killed him on the Ponderosa.

Jennifer Beale is abducted in the hopes her rich father, Joshua, the richest silver baron on the Comstock, will pay a $1M ransom. The plan unravels when the beautiful Della is killed and Hercules, who loves her, finds out who did it.

Dolly Kincaid is so fed up with her extremely dominant, controlling, sheriff father, that she runs away with her boyfriend. She later finds out he is the leader of some murderous bank robbers and when they kidnap Hoss and Joe, she still sticks with him.

About to set out on a cattle drive, Ben hires a young drifter named Sam Jackson as one of his drovers. What he doesn't know is that Jackson is really outlaw Johnny Logan, who signed on to the drive because he knew it was going to pass near the town of Waycross, and Logan is determined to kill the Waycross sheriff--who is his father.

Adam rides up on some Indians wanting to harm a white woman they believed was a mountain spirit. He kills them but not before they wound him. The woman nurses him back to health but the rest of the tribe is still out there looking for her.

An English couple comes to Ponderosa on vacation, but the wife slowly makes it clear that she is disappointed that her husband, a great hunter and "action man" is becoming more peaceful, and not the man she married, though things may change for her after they are kidnapped for ransom along with Adam Cartwright.

Angry with the way a beautiful deaf-mute girl is treated by her father, a sheepherder living in a remote mountain cabin, Little Joe takes it upon himself to teach her sign language so they can communicate better. His plan backfires when the young woman falls in love with him and the girl's brutish neighbor resents her lavishing attention on the youngest Cartwright.

Hoss mentors a lonely, mentally challenged man who, with superhuman size and strength, becomes extremely dangerous when angered. These efforts are undermined by a saloon girl who only wants this giant man-child to manipulate him.

When 16-year-old Todd Grayson arrives from Boston to Virginia City, he is told that his father has been killed by Ben Cartwright. Ben shot Luke Grayson in self-defense, but Todd won't listen to this. The boy has only one thing in his head: to avenge his father by killing Ben Cartwright.

Hoss falls prey to the wiles of a beautiful woman with a gambling addiction and refuses to believe she's only interested in his money in spite of Adam's proof to the contrary.

After Joe kills a man in self-defense who tried to set fire to the Ponderosa to clear himself some land, he has to take his lively, feisty, wild daughter home, and she and her relatives are now determined to kill Joe.

Bill Hawks receives a note asking him to help an Indian friend of his from the Civil War. He arrives to find the local town drilling a well on the man's property and eventually that the man has been hanged for attacking a local girl.

Bill spots a young boy alone on the trail. He passes out but they later learn he can't talk but that he saw his dad killed by strangers for no apparent reason. Later, they run into Dr. Denker taking musical instruments to California.

Duke comes across Malachi Hobart, a preacher dedicating his life to his fellow man, and is impressed with his charitable works. However, he begins to believe that the pastor is in fact a con artist who is using religion to swindle people.