Plumfield School for boys is still recovering from the death of its headmaster, Fritz Bhaer. Parents aren't happy to find their sons in a school run by a woman, and many are removing or threatening to remove their sons. The grounds are in a state of disrepair, and the student teacher is due to leave to Harvard soon. The school needs a professor, a handyman, a strong male role model and more students. Headmistress Jo Bhaer needs more time -- or a string of lucky breaks.

A wanderer named Nick Riley hears in town that the school needs a handyman, so he shows up and gets right to work. He's a merchant marine and he's waiting for a ship scheduled to leave from Boston harbor in just over a week. Jo decides that a short-term arrangement is low-risk, so she accepts his offer. But she questions the decision when Nick distracts the children with his tales of adventure and disrespect for "book learning".

Jo turns down a chance to sell the school. Her sister, Meg, points out that the school has lost four students, and prospects for new students are dim. Jo improves her prospects by enrolling Nan, the school's first girl. Nan is a tomboy who is eager to prove herself equal to the boys in her ability to work and compete.

While Jo interviews potential teachers, Nick takes the children out to pick huckleberries. Nan challenges Dan, an impulsive, outgoing ringleader among the boys, to a berry-picking contest, then to a series of foot races. Eventually, Dan falls and twists his ankle. Nan doesn't know which way to go for help, and Dan doesn't recognize where they are, either. Sunset is approaching, and the children are lost.

The other children tell Nick that sometimes they pick berries all the way home. Nick presumes that's what Nan and Dan have done. He loads the wagon and returns to the school; Jo wonders where the other children are. Jack and Tommy arrive on foot lugging pails filled with berries. No, they didn't see Dan and Nan. Jo quickly saddles a horse and heads out to find them. Nick follows suit.

When they find the children, Jo decides that Dan's injury is punishment enough. Nan expects a whipping, but instead, Jo ties a "leash" of yarn around her waist, and the other end to her bedpost. Nan starts to untie the yarn as soon as Jo leaves the room, but she hears Jo calling her an honorable girl who can be trusted to accept punishment.

Nick, stinging from Jo's chastisement for letting the children get lost, has packed his bags and is on his way. He passes Emil, a student whose uncle pulled him from the school. Emil is bruised from his uncle's beating. He was being sent to military school when he jumped the train and came back to Plumfield.

Farther down the road, Nick meets Emil's uncle and other parents headed to the school. The parents are intent on taking their children, but the students' impassioned defense of the school, plus the instructor's agreement to delay college until a suitable replacement can be found, convinces the parents to give Plumfield another chance.

Emil's uncle remains unconvinced. He tries to physically remove Emil from the classroom. Suddenly, Nick appears and tells the uncle to leave Emil alone. He shoves Nick, who responds with a punch that floors the uncle.

Nick is arrested for assault, and Emil's uncle tries again to take him from the school. Jo says that if Emil doesn't receive at Plumfield the kind of education the uncle expects, she will refund his entire tuition. That convinces the uncle to leave Emil and give the school another month to prove itself.

Jo arranges to have Nick released to her custody for the duration of his sentence. Looks like he'll miss that boat leaving Boston Harbor. Jo discovers he's been jailed before, and says she'll send him back unless he's on his best behavior at the school.