While visiting a remote town to await the arrival of Ben, Little Joe and Candy, Hoss is wrongly arrested for the murder and robbery of a hermit miner. When a lynch mob starts to gather, cowboy Child Barnett breaks Hoss out of jail. Both are chased by a posse whose interest is not justice, but the retrieval of the money that the miner was thought to have stashed away.
Candy relives his past when he and the Cartwrights help a Cavalry unit that is pinned down by bandits. In that Cavalry unit is Candy's ex-wife, who he still has feelings for. Her new husband is the Captain of the unit.
Ben sells a prize bull to an old friend, whose unscrupulous son has taken charge of the ranch from his father. The son double-crosses Ben over the agreed price of the bull, only offering to pay well below the selling price. Upset over the deal, Ben stays in town to seek proper compensation.
While in small town Tin Bucket to sell Ponderosa cowhides, Candy is accused of cheating in a card game and the Cartwrights are dogged by a mysterious rumor that claims they have fallen on hard times and are desperate for money.
A white woman, abducted by the Paiutes and thought to be dead, is brought back to Virginia City and reunited with her husband. When it is found she has an Indian baby to a Paiute chief, she is outcast by the towns people and her husband alike. Only the Cartwrights remain her friends.
Brand new U.S. citizen and vintner, Georgio Rossi, riles his neighbors and risks government wrath when he allows an Indian family to break treaty and camp on his land; meanwhile, Candy woos pretty Regina Rossi, stirring up some trouble of his own when she and her mother try to take over the smitten ranch hand's life...and Hop Sing's kitchen!
Ben's friend Beaudry visits the Ponderosa, meets Noreen, a beautiful girl at the Virginia saloon, gets into a roust, ends up in jail but Ben gets the instigators to own up and pay for the damages, so he is free. He asks Ben Cartwright for help starting a cattle ranch, without revealing his rustling and political crimes. Deputy Stryker comes to Virginia City from Montana with a warrant looking for Beaudry.
A town bully humiliates Hop Sing by cutting off his ponytail. Joe goes into town to deal with the bully. Later the bully ends up dead and Joe is charged with the murder. Hop Sing clears Joe of the murder charges by using an ancient Chinese method for identifying a person's finger prints.
At an old friend's request, Ben agrees to shelter a witness in a government case. He's a witness to several felonies and they've tried to kill him several times already. When he asks to see his wife, he puts them all in danger since she is being watched.
Hoss is rescued from a band of hungry Paiutes rustling Ponderosa cattle after a hard winter by Erin O'Donnell, an Irish woman who was raised by the Sioux and revered by the tribes as a medicine woman and mystic.
Candy is kidnapped by retired Army Sergeant Mike Russell and his band of fellow former soldiers when he uncovers their plan to blast their way into the Carson City Mint to steal the pension they believe they deserve, but never received, from their long years of Army service
Ben Cartwright's effort to help friend Ruth Manning defend her ownership of nearby Gunlock's town newspaper, the Clarion, earns him the wrath of a corrupt, powerful judge who wants the Clarion for himself and will do anything to get it.
Ben and the other ranchers are having trouble with a Mountain Lion killing cattle. Ben and Roy go in hunt of the Lion because Hoss and Joe think they both are sparking the magician's daughter. It's causing rivalry and confusion unaware they're sparking twins.
A seasoned Army Sergeant escapes from the stockade accused of cowardice in the face of the enemy. A man helps him escape, is killed and he is shot. Candy stumbles on him and his squaw wife he believes him and decides to help but an Army search party isn't far behind.
Ben and Hoss are brought under siege with their friend, Sam Masters, and his daughter, Ellen, in an isolated miner's cabin by a former Union Army officer and his men who claim that Sam is really Confederate prisoner of war camp Commander Thomas Andrews who is guilty of Civil War crimes and on the run.