Bonanza's twelfth season commenced on September 13, 1970 with the episode titled "The Night Virginia City Died." Several Virginia City buildings have burned to the ground; the townsfolk are in an uproar, and the local constabulary is apparently helpless. Meanwhile, the Cartwrights have befriended a pretty young stranger named Janie (Angel Tompkins), the new sweetheart of Deputy Clem (Bing Russell). Only the audience knows that the profoundly disturbed Janie is the elusive arsonist whom everyone is seeking. Written by John Hawkins, this episode was specially contrived to "destroy" the old Virginia City sets at the Paramount studios so that the Bonanza company could move into its new home at Warner Bros. "The Night Virginia City Died" also boasted a new Bonanza theme song by David Rose, which would endure until the old theme was brought back by popular demand in 1972.

Originally telecast September 20, 1970, "A Matter of Faith" served to introduce new Bonanza regular Mitch Vogel in the role of Jamie Hunter. The son of an itinerant rainmaker, Jamie is unofficially adopted after his dad's death by Ponderosa hand Dusty Rhodes (Lou Frizzell. Despite the skepticism and outright hostility of the townspeople, Jamie is determined to fulfill his father's promise to bring rain to drought-stricken Virginia City. "A Matter of Faith" was written by Jack B. Sowards, John Hawkins, and former Star Trek scrivener D.C. Fontana.

Robert Pirosh's teleplay for this Bonanza episode was based on an actual 19th century phenomenon. In the years following the Civil War, many young and disillusioned ex-soldiers formed nomadic groups called the "Weary Willies", who roamed throughout the west living off the land and avoiding "proper" employment. In other words, they were the hippies of their time, something with which viewers could instantly relate when this episode first aired on September 27, 1970. In the course of the story, the Ponderosa welcomes the Willies to their property, but their neighbors do not. When a girl is attacked, the Willies are accused of the crime, but the truth lies closer to home. The cast includes a pre-Waltons Richard Thomas as Billy, Lee Purcell as Angie, Elisha Cook Jr. as Marcus, and Kevin Tighe as Krulak. In keeping with its flower-child ambience, "The Weary Willies" features several songs, including "Man Passing Through", "Blood Brothers" and "It Won't Be Very Long".

When one of his prisoners escapes, sadistic prison-wagon boss Price Buchanan (Denver Pyle) abducts Hoss Cartwright and forces him to take the missing convict's place. Facing five years at hard labor, Hoss formulates an escape plan with another railroaded prisoner, Madge Tucker (Salome Jens). Others in the cast included George Murdock as Stuart Getty, Jonathan Lippe as Kyte, Lee Jay Lambert as Jase, Stuart Randall as Sheriff Brody, and Bob Vanselow as Fred Quinn. Written by Ken Pettus, "The Wagon" originally aired on October 5, 1970.

Rupert Crosse guest-stars as Davis, a fugitive killer. While searching for Davis, Joe and a seriously wounded Ben are stranded at a desert water hole with the escapee. As Ben's life slowly ebbs away and a band of renegade Indians close in, Joe heads into the desert on foot to seek help-forcing him to place his trust in the mercurial Davis. First broadcast on October 11, 1970, "The Power of Life and Death" was written by Joel Murcott.

Guest star Richard Kiley is cast as Sheriff Gideon Yates, one of Nevada's most admired lawmen. When Joe Cartwright comes to Yates claiming that he has witnessed a murder, the Sheriff realizes to his horror that the killer was his own wife Lydia (Terry Moore). With grim determination, Yates quietly decides that Joe must be silenced for keeps, leading to one of the most thrilling showdown sequences in Bonanza history. Written by Ken Pettus, "Gideon, the Good" was first shown on October 18, 1970.

"Trouble" is the apt cognomen for one of the toughest towns in California. Through a fluke, Hoss Cartwright is named temporary sheriff of Trouble, determined to do his duty even though the citizens want nothing to do with law and order. Through methods both persuasive and pugnacious, Hoss ends up arresting virtually the entire town! Also in the cast are Gene Evans as Montana Perkins, G.D. Spradlin as Chip, E.J. Andre as the Judge, Jeff Morris as Matthew Brody, and Hal Holmes as Mark. First seen on October 25, 1970, "The Trouble with Trouble" was written by Jack B. Sowards, who penned many of Bonanza's funnier installments.

Far from the Ponderosa, Ben Cartwright is badly injured in a fall from his horse. Seeking help in a nearby town, Ben's son Joe finds himself in the middle of a range feud, with no one willing to come to his assistance-except for an enigmatic stranger named Thornton (played by frequent Bonanza supporting actor Gregory Walcott). Written by Preston Wood, the episode is highlighted by a jaw-dropping nightmare sequence which still packs a jolt after all these years. "Thornton's Account" was originally broadcast on November 1, 1970.

Carol Lawson plays Etta, an unwed mother determined to carve out a decent life for her son Scott (Michael-James Wixted). When she learns she is dying, Etta asks her long-estranged parents to look after Scott-but her stern and merciless father Zac (Will Geer) is unwilling to do so. Josephine Hutchinson rounds out the supporting cast as Etta's mother Martha. David Rose's evocative musical score won him an Emmy Award. Originally shown on November 8, 1970, "The Love Child" was written and directed by Bonanza star Michael Landon, who in 1985 reworked the story as "A Child of God," an episode of his later series Highway to Heaven.

Aranda (Rodolfo Acosta, the Mexican-born sheriff of Prince River, regularly betrays his own people by participating in a land grab perpetrated by ruthless miner Owen Driscoll (Warren Stevens). The Cartwrights become involved when Aranda frames Mexican farmer Ramon Cardenas (Jaime Sanchez) for murder, the first step in Driscoll's scheme to buy out the other farmers for ridiculously low prices. A shocker ending caps this Bonanza episode, which was written by Ken Pettus and Dick McDonough. "El Jefe" first aired on November 15, 1970.