Matilda The Musical JR. opens with enthusiastic school children (and their equally enthusiastic parents) singing their own praises... except MATILDA. According to her parents, she is nothing but a nuisance (Miracle). At Matilda’s home, her father, MR. WORMWOOD, reveals his scheme to sell old automobiles as brand-new luxury cars to Russian businessmen. Matilda doesn’t believe this is fair and goes to her room, pausing on the way to mix her father’s hair tonic with her mother’s hair dye (Naughty). The next morning, Mr. Wormwood’s hair is green.
Matilda drops by the library to visit MRS. PHELPS, the librarian. She tells Mrs. Phelps part one of the tale of the ACROBAT and the ESCAPOLOGIST, two circus performers deeply in love. The tale cuts off just as the couple is primed to perform their most dangerous trick. Matilda starts her first day of school the next morning (School Song). Fortunately, Matilda’s teacher MISS HONEY, a woman who cares deeply for her students. MIss Honey immediately recognizes Matilda’s advanced intelligence, prompting her to visit the school’s vicious headmistress, MISS TRUNCHBULL. The teacher hopes to promote Matilda to a more challenging class, but Trunchbul refuses (The Hammer).
At the Wormwood home, Miss Honey tries to explain to MRS. WORMWOOD how special her daughter is, but she doesn’t listen, returning to her dancing lesson with RUDOLPHO. Miss Honey feels helpless (This Little Girl). At the library, Matilda continues the circus story for Mrs. Phelps. The Escapologist announces that their act is canceled because his wife, the acrobat, is pregnant. However, the Acrobat’s sister refuses to cancel the act.
At school the following day, Truncbull bursts into the classroom, accusing Matilda of eating a piece of her cake - but the culprit turns out to be BRUCE. Trunchbull punishes the boy by forcing him to eat the rest of the cake in one sitting, and the kids cheer as he finishes the cake (Bruce - Part 1). Despite his victory, Trunchbull takes Bruce to the chokey Matilda is upset by the unfairness of this. She goes to the library, launching into the next part of her dramatic circus tale. The Acrobat is killed during the performance - but not before giving birth to a baby. The children in Matilda's school sing about what life will be like when they grow up. Miss Honey and Matilda join in (When I Grow Up).
At the Wormwood home, Mr.Wormwood announces that by tweaking the speedometers in his cars, he has completed a successful business deal with the Russians. Matilda is disgusted. In her room, Matilda finishes the story: the Escapologist leaves to confront his treacherous sister-in-law, but never returns.
The next day at school, Trunchbull believes the students are up to something (The Smell Of Rebellion). Her fears are confirmed when LAVENDER puts a newt into Trunchbull's water jug, causing pandemonium. Everything slows down as Matilda explains to the audience that she can sometimes find calmness in herself that allows her to do amazing things (Quiet). She uses her ability to throw the glass with the newt at Trunchbull who screams and runs. Matilda reveals her ability to Miss Honey, who admits that she is poor and lives in a shed. Her father died when she was little, and her cruel aunt became the owner of her childhood home. Miss Honey suspects her aunt killed her father, and reluctantly reveals that her aunt is none other than Trunchbull.
The next day, Trunchbull challenges Miss Honey’s class to a spelling test. The students spell every word right. When Trunchbull claims a student has misspelled a word and tries to drag her to the chokey, the whole class begins spelling incorrectly in solidarity. Writing appears by Trunchbull’s dead brother in law but actually magically written by Matilda. Trunchbull leaves and the children sing in joy (Revolting Children).
Miss Honey inherits her parents house and takes over the role of headmistress. Just before Matilda is whisked off to Spain by her family who are on the run from the Russian mob, Miss Honey has a proposition: Let Matilda stay with her. The Wormwoods agree, and Matilda and Miss Honey are both overjoyed (Bows).