Smedley football team, the Tornados, is notoriously awful and slacking, much to the dismay of the entire school. The students humor her, opting not to talk about Miss Swamp, but they ponder why Miss Nelson didn't see her in the hallway. A moment later, the real Miss Nelson cheerfully returns. Blandsworth brushes it off and exits, and Miss Swamp warns the class never to pull a stunt like this again, and she exits herself. Blandsworth enters, and feigns surprise, when he claims she's being impersonated. She then sees the Miss Nelson mask, and calls them out on their deception. It doesn't take much effort for her to put the class back on track with proper behavior, and catching up on schoolwork. While the students are slacking off enjoying themselves, who should enter the classroom, but Ms. Blandsworth dismisses her claiming 'Miss Nelson is back!' leading her to take action. However, they unknowingly walk past Miss Nelson's house, where the real Miss Nelson sees them.

This Miss Nelson takes the students to the movies, and later to the ice cream parlor. Blandsworth into thinking that Miss Nelson has returned early. Three students are able to create a makeshift Miss Nelson, with a costume and a mask, and manage to fool Mr. However, he turns out to be extremely boring, and the students plot to get rid of him. Blandsworth will be acting the substitute teacher. The students fear the worst the following week, but their mild-mannered principal, Mr. Her students plan on acting up like never before for that week, until an older student warns them about the notoriously strict substitute Miss Swamp. Miss Nelson announces to her class that she will be having her tonsils removed and will be out for the following week. At the end of the film, it is revealed that Miss Viola Swamp was Miss Nelson in disguise, and a police detective has called off his search for Miss Nelson and will now look for this enigmatic Miss Swamp. After many days of tyranny under Miss Swamp, Miss Nelson returns to class and the children rejoice, now being more respectful of her.

The contrast between the two teachers is so great that the students actively go looking for Miss Nelson and make unlikely conjectures about what may have happened to her, including some students who go so far as to fill out a missing person report with the local police. Swamp is a strict disciplinarian and gives the students significantly more school work than Miss Nelson ever did.

However, before they get the chance to make mischief, a substitute, Miss Viola Swamp, shows up. The students decide that, without a teacher, they can misbehave all day. But then one day, she does not come to school. After their constant misbehaving and rudeness, and their refusal to learn, Miss Nelson determines something has to be done. Miss Nelson is a grade-school teacher whose students constantly take advantage of her nice nature.

Miss nelson is missing by harry allard