When Sully opposes the construction of a nearby dam, he finds himself on the other side of the law and behind bars. Sully joins forces with Preston to try and peacefully stop the dam construction which will mean the end of hundreds of acres of countryside. But when Sully hears that the men Preston's hired to hijack a shipment of dynamite are determined to kill any witnesses, Sully rides with them in order to prevent the murders. However, when witnesses attest to the fact that Sully was riding with the hijackers, Matthew is forced to arrest him and Sully must go to court where Judge Webster finds him guilty and throws him in jail, creating discord in the family.

On a visit to Colorado Springs, Dr. Mike's revered Uncle Theodore shocks her and Sully by criticizing their parenting skills with regard to Brian and offering to take Brian back with him to Boston. Brian considers leaving his family when Theodore, a concert pianist, recognizes the boy's musical talent and tempts him with visions of becoming a concert pianist in Boston. Actually, Theodore dislikes what he considers to be the "liberal attitudes" of Sully and Dr. Mike that he feels put Brian in danger. When Brian is injured while on the trail with Sully, Theodore can no longer hide his feelings and Dr. Mike realizes that her uncle is attempting to replace his own lost son with Brian.

Dr. Mike sees that the marriage of Kid Cole and Sister Ruth is unraveling and the couple is heading for divorce for no apparent reason. Johnny Cash and June Carter Cash reprise their roles as Kid Cole and Sister Ruth. When Cole and his wife stop to see Dr. Mike while escorting mail-order brides to San Francisco, Dr. Mike immediately feels the tension in the air between them. She then learns that Cole is terminally ill and, in an attempt to spare Ruth the agony of watching him die, has created problems in their relationship so Ruth won't feel obligated to care for him. Ruth, meanwhile, is devastated at her husband's behavior and talk of divorce and seeks Dr. Mike's advice.

When Colleen, who is working on a college paper, asks Dr. Mike to recall her most memorable case, Dr. Mike looks back on the five turbulent years she's lived and loved in Colorado Springs. As they sit with Andrew, who is mysteriously ill at the clinic, Dr. Mike reminisces about her tumultuous career -- its successes and its failures -- and realizes how many divergent cases she has seen and treated. When Andrew's condition takes a turn for the worse, Dr. Mike warns Colleen about the fine line between emotional involvement and professional detachment, an issue with which she has long struggled in the frontier town that's now her home.

Sully's best friend Daniel arrives for a visit, but the relationship becomes strained when Daniel offers Sully money at a time when Sully desperately needs it to save the homestead.

After Preston calls the loan due on the homestead while Sully is gone, Dr. Mike reluctantly accepts Daniel's offer to pay it off, further straining relationships. Things are also complicated because Daniel has fallen in love with Dr. Mike.

Dr. Mike, Brian and Katie are taken hostage at the homestead by bank robbers, one of whom is wounded. After Dr. Mike is taken hostage by Brent and Huston, she watches helplessly as Sully, returning from a trip is shot by Brent as he approaches the house. In spite of his injury, Sully, with the help of Wolf, Cloud Dancing, Matthew, Hank and Andrew, plots a rescue plan. Meanwhile, inside the house with the two desperate robbers, Dr. Mike and Brian do some quick thinking and - with the help of some chloroform - distract the men while they scramble to come up with an escape scheme of their own.

Dr. Mike and the townspeople excitedly welcome the famous writer and poet Walt Whitman to Colorado Springs until rumors about his personal life begin to circulate. When Dr. Cook brings to light the rumor about Whitman preferring the company of men, Preston, who is playing host to Whitman, abruptly cancels the poet's reading, the townspeople shun him, and even Dr. Mike finds herself acting with suspicion when she learns that Whitman has taken Brian under his journalistic wing.

When he gets the papers for his divorce from Myra, Horace attempts suicide and almost succeeds. His friends do what they can to help him, but it turns out that depression isn't always cured that easily.

Michaela gets a surprise visit from her sister Marjorie, who turns the town upside down with her radical ideas. But even though Michaela partly agrees with Marjorie, she has to ask her to start thinking about other people's feelings.

Sully and Brian forge a true father-son bond when Brian's free-wheeling, irresponsible adolescent behavior puts him in mortal danger, and Sully disciplines him. As Brian's adopted father, Sully has let Michaela set the rules for Brian up to now. But when Brian's misbehavior with his friend Anthony puts them, and the town, in danger, Michaela and Sully realize that Brian needs -- and wants - Sully to act as Brian's real father and give the boy the boundaries he needs, which enhances and strengthens their bond.

After Cloud Dancing is beaten almost to death, Sully organizes an escape for him and the others on the reservation, which turns deadly. Sully flees with a price on his head.

Sully tries to get Cloud Dancing to safety in the north. The actions of the renegade dog soldiers take their toll on the town. An old enemy goes after Sully and Cloud Dancing.

After Sgt. O'Connor is found dead at the bottom of a cliff, everyone fears that Sully died too in the fall. Dr. Mike and friends go looking for Sully. Matthew quits as sheriff. The Dog Soldiers continue raids on the town.

Dr. Mike, Matthew, Brian and Daniel find a seriously wounded Sully and move him to a cave near the homestead so they can nurse him back to health while hiding him. Dr. Mike starts working to clear Sully's name.

General Wooden is injured by dog soldiers and dies. Daniel talks with Sgt. McKay and the non-violent Indians are let free. Hank takes over as sheriff temporarily. Daniel runs for sheriff and wins. Sully and Cloud Dancing work for peace.

While Sully is gone up north trying to convince the Dog Soldiers to stop fighting, Dr. Mike finds out she is pregnant. But she suffers a miscarriage and feels all alone with Sully gone. The town celebrates Founder's Day.

Dr.Mike becomes alarmed when a Russian Princess is a guest of Preston's hotel & claims she has a gift to speak with the dead.

Dr. Mike worries about how to tell Robert E. and Grace that their adopted son Anthony may not survive his mysterious illness. Meanwhile Sully struggles with convincing the renegade braves to return to the reservation and learning about Dr. Mike's recent miscarriage.

Marjorie, Dr. Mike's sister returns to town as a member of the Women's Temperance League to try to outlaw alcohol. Jake starts believing that there may be something going on between Hank & Ms. Teresa. Meanwhile Grace has turned to drinking to help comfort the recent death of her adoptive son Anthony.