In the 12th season premiere, a series of destructive fires strike Virginia City, and always late at night. Is it the work of a ruthless arsonist, or someone very close to Deputy Clem?

Dusty takes in orphaned Jamie Hunter, the son of a recently-deceased rainmaker. Jamie is determined to carry on his father's tradition by using drought-stricken Virginia City to prove his talents.

After being taken into custody by a sheriff who does not care if he is guilty or innocent of a crime, Hoss escapes from the prison wagon with a woman he is convinced got a raw deal.

A man called Davis has shot Colonel Clayton and escapes on horseback. Joe and Ben join the posse that sets out to find Davis. Ben and Joe volunteer to cross the desert. Ben and Joe find Davis hold up at a water hole, when Indians attack and Ben is wounded in the leg, and steal the horses. Joe unties Davis, who tends to a wounded Ben, who is suspicious that Davis will try to escape. After playing a game of cat and mouse, Ben and Davis come to an agreement: survival. Joe makes the decision to cross the desert on foot, while Ben and Davis are at the water hole, both men in need of medical help and justice.

On the trail, Joe witnesses a woman kill a man, but the woman rides away before he can positively identify her. He rides into the nearest town, Black River and reports the crime to Sheriff Gideon Yates, and the two ride out to find clues. They find a handkerchief embroidered with the letter "L". Sheriff Yates knows who the killer is, his wife Lydia. She married him before she got a legal divorce from her first husband, Loomis, and killed him to silence him. Gideon tries to coax Joe out of town, but he recognizes Lydia's picture in a photographer's window. When Joe refuses to leave, Gideon tries to shoot him down in cold blood and orders a manhunt against him. Joe's only hope is a Mexican stable boy, who saw Gideon shoot him, and ultimately Joe and Gideon have one of the most memorable confrontations in the series' history.

When Hoss volunteers to be Sheriff of a town called Trouble, he soon finds out that the town had correctly been named. Hoss almost manages to arrest the whole town, and captures the Clanton gang all by himself.

Ben's new horse throws him down a steep slope, injuring his back. Joe tries to round up some help, but the settlers in the valley live in fear of the devious owner and his hired help. Joe goes for help from a man named Thornton, but he is wounded by the lowlife cowboys, and has no choice but to ask them for help. A very imaginitive and visually creative dream Ben has of Joe calling out to him and falling beside him, before waking up and realizes he has just had a terrifying nightmare.

A dying woman and her son are rejected by her father because she had a child out of wedlock.

Ben and Hoss come to the rescue of Mexican farmers who are forced off their land by the greedy mine owner who runs the town of Prince River.

Pepper Shannon is a dime novel hero and outlaw. Ben gives a job to Pepper Shannon on the condition the one-time outlaw stays away from Jamie, who happens to admire him.

Hoss and Joe pretend to be stage robbers' partners in order to recover stolen Cartwright money. All goes well until the wife of one of the thieves shows up.

Jamie forms a bond with a bum and his tame crow. Before long, Jamie suggests they repair an old wagon and leave the Ponderosa.

A girl's uncle and aunt want custody of her only because they believe she has the rights to her late grandfather's mine.

Settlers from Virginia argue over Hoss' fate after one of them accidentally shoots him.

An insecure Jamie is unsure of his place in the family, having trouble adjusting at his new school and keeps getting harassed by a bully. When he takes Ben's prized gold-plated rifle and breaks it, he runs away, sending Ben to go looking for him.

The Cartwrights are about to start a major cattle drive with other ranchers. It has been decided that Ben's foreman will be trail boss on the drive. Weatherby, a fellow rancher who is also with Ben, has agreed to have Kelly as trail boss, until he finds out that Kelly was previously on a cattle drive with him, and fired him for drinking. Weatherby also suggests that his younger wrangler take the job as trail boss, and a conflict is started between both Ben's foreman and Weatherby's wrangler.

Bradley Meredith, a Ben Cartwright look-a-like, causes trouble when he sells land to the railroad. Ben has already turned down the deal, but Meredith, acting as Ben, accepts the deal, which stirs up all kinds of trouble.

Hoss is held prisoner by a fugitive black couple who they admit hate white people and have nothing to lose by killing them.

An English couple comes to Nevada to learn why a ranch owned by the British investment firm is the only company holding not showing a profit.

Ben is shocked to learn the Army general he is backing as governor, advocates a policy of genocide towards all Indians.

An epidemic of influenza hits the Ponderosa and the only person who seems sure of what to do is the wife of a doctor, whom Doc Martin says is a fraud.

A racist and his henchmen steal a Gatling gun, with plans to massacre everyone - including the Cartwrights - involved in a peace treaty signing between the U.S. Army and the Paitues in Virginia City. The man's hope is that the tragedy will spark another war and eventually lead to the genocide of all Native Americans.

Blinded by an explosion, Joe wallows in self-pity, and at first resists the efforts of a woman trying to teach him to live without sight, not knowing she is also blind.

While visiting the Ponderosa, Ben's friend, April Christopher, is bitten by a rabid wolf. Ben and April and her daughter must come to terms with her illness as they all realize the terrible fate that awaits April.

The foreman of a neighboring ranch shoots a special steer belonging to the Cartwrights, and his scheming boss plots to take unfair advantage of the mistake.

Ben, Hoss and Joe, along with Candy and a fellow rancher, are jailed on false trespassing charges by a greedy mining tycoon. The despot runs a gold mine (i.e., a thinly-veiled prison camp) and acquires slave labor by pressing phony criminal charges against the unfortunate inmates.

The only person who can get Dusty out of jail is a professional fighter who will not return to Virginia City, so Joe stays on the man's heels no matter where he goes.