Dr. Mike takes in Red McCall, a down-and-out cowboy, and his ailing half-breed infant child. McCall reaches the end of his rope trying to care for his baby, so after robbing Loren's store, he leaves the baby in Michaela's care, sensing she could find a suitable home for his child. Dr. Mike's attempts to find a home for the baby prove futile.

When she travels to a remote cabin to check on the health of it's owner, she finds him badly mangled from a bear attack. Her horse is frightened off by the bear, and she's marooned in the cabin until Sully shows up looking for her. They narrowly escape being the rabid bear's next victims.

After returning to town, Dr. Mike decides she'd rather raise the child herself than turn him over to an orphanage. However, Sully locates Red and convinces him to keep the child.

An old friend of Sully's visits, wanting to financially help the family. Although he falls in love with Michaela.

While Sully is away for a few days to procure some money, Preston arrives threatening to repossess the homestead for nonpayment of the load. Daniel rejects Dr. Mike's objections and pays off the entire loan. Upon hearing how Daniel interfered in his business, the proud Sully becomes furious.

Sgt. O'Connor was found dead in the river. Sully is nowhere to be found. Michaela believes that he survived and goes looking for him. Daniel comes to offer his help. Dorothy and Cloud Dancing share their first kiss.

Sully is found alive, but badly hurt. As Michaela nurses him back to health, she keeps him hidden from the army. Sully sneaks into the homestead one night to spend time with his wife.

Sully is wanted for treason and murder. In order to keep him safe, Michaela pretends that Sully is dead and has a memorial service for him. Hank and Jake find out Sully is alive. Cloud Dancing and Sully meet with Black Moon.

Russian Princess Nizamoff (Natasha Andreichenko) who claims to see the future, tells everyone what they want to hear. Even Michaela is taken in by her.

A diptheria epidemic sweeps through C.S. Michaela performs a procedure that is not a proven cure. Becky (Haylie Johnson) dies.

Mrs. Quinn wants to take to the children to Boston with her. She also disapproves of Loren and Marjorie's relationship. Marjorie contracts the illness. The family sneaks Sully home for Thanksgiving.

Dorothy discovers the deed to the property that Grace's cafe is on. Hank accidently breaks Horace's nose and won't pay for the damage. There is a sudden rash of lawsuits and Michaela acts as Judge.

Consumption hits Black Moon and his men. Black Moon agrees to surrender in exchange for safe passage of his men to protected land. Michaela negotiates the deal and asks also that Sully be pardoned.

Sully and Michaela are on their way home for Christmas, when they stop to help a couple inexperienced in the wilderness.

Chinese immigrants set up camp. Dr. Quinn discovers a young woman (Yumi Iwami) posing as a man in order to practice medicine, which is forbidden in her culture. Her Grandfather (Robert Ito) is stunned, but supportive.

Hank captures Cloud Dancing and gets the army to send him to a reservation far away. Jake and Teresa marry, despite her aunt's (Carmen Zapata) disapproval.

Michaela worries about Brian's friendship with an eccentric man (Martin Von Hoffman) who thinks he is a bird.

U.S. Marshall Elias Burch (guest star Willie Nelson) asks Matthew, still a student of law, to defend him when he's accused of murder.