Rafe Khatchadorian, who enjoys a passion for art and has an incredible imagination, transfers mid-semester to Hills Village Middle School after being kicked out of the only two other schools in the entire district that would accept him. On his first day, he meets the strict and exceedingly vain Principal Ken Dwight and his obsequious Vice-principal, Ida Stricker. Dwight forces students to comply with an extensive list of rules that are mostly senseless while Stricker follows along with his antics. Later that day, an assembly focused on the BaseLine Assessment of Academic Readiness (B.L.A.A.R.) standardized test, led by Dwight, is interrupted when another student grabs Rafe's sketchbook in which he had drawn the principal as a zombie repeating "B.L.A.A.R." over and over. Dwight responds by destroying the sketchbook in a bucket of acid, much to the devastation of Rafe.
Later that day, Rafe is back in his room with his best friend, Leo, who suggests that to get even, Rafe should destroy Dwight's rule book. To show the ridiculousness of Dwight's rules, Rafe and Leo pull several pranks such as papering the walls of the hallways as well as Dwight's office with colored sticky notes, rigging the period bell to make it end with a fart, filling the teachers' lounge with plastic balls, putting pink hair dye in Dwight's hat, and turning the trophy case into a fish tank, complete with an eel. These pranks gain the attention and admiration of Rafe's fellow students, including Jeanne Galletta, on whom Rafe develops an immediate crush.
In the chaos, Dwight, obsessed with his school's performance on the B.L.A.A.R., realizes that if he can exclude the remedial class, which includes Rafe, from the test, then the average scores will improve. Dwight frames several students from the class by secretly putting items in their lockers that make it appear like they were responsible for the pranks and suspends the whole class for a week, and even uses the opportunity to unlawfully fire Mr. Teller, the compassionate remedial class teacher who, along with the other teachers, disagrees with Dwight and Stricker's antics and sees through Dwight's plan. Rafe immediately goes to Dwight's office and begs him to not suspend the other students since he was the one responsible for the pranks; when Dwight refuses, Rafe creates a wild dance party via the sprinkler system and fire alarm,soaking the school and the students in colored dye that was intended to be yet another one of his pranks, which prompts an enraged Dwight to expel Rafe permanently.
Now expelled from Hills Village Middle School, Rafe is confronted by his mother Jules who tells him that her fiancé Carl "Bear", who seriously loathes Rafe and his sister Georgia, has found a military school where Jules should consider sending him. While acknowledging that it is not ideal, it represents what may be the only option left. She also pauses to reflect the passing of Rafe's younger brother Leo, revealing that Leo had been imagined the whole time by Rafe. Later that evening, Jeanne shows up at Rafe's house with evidence: a VHS Tapes containing a documentary of the school she had recorded with surveillance footage of Dwight putting the items "found" in the student lockers himself to frame the students so that they would get suspended and the test would be rigged. With this evidence, Rafe, Jeanne, and Georgia gather the suspended students from the remedial class outside the middle school, along with the janitor Gus, who also dislikes Dwight's rules, and pull together a plan to get revenge on Dwight and Stricker.
The next morning, Jules discovers that neither Rafe nor Georgia are home and becomes concerned about their disappearance, but when Bear shows more concern in the fact that his car is missing as it was stolen by the kids, she finally realizes that he is nothing more than a "selfish jerk".
Meanwhile, with B.L.A.A.R. testing ready to begin, Rafe and his classmates interrupt procedures and expose Dwight's deceitfulness. Gus shows up in a cart to pick up Rafe while Dwight gives chase, only to have a pile of manure dumped all over him. Just as Dwight catches up with Rafe and Gus, Mr. Teller arrives with superintendent Hwang whom Rafe hands over the video proving Dwight's guilt. After viewing the video, Hwang fires both Dwight and Stricker for creating unlawful rules, illegally rigging the B.L.A.A.R., unlawfully firing Mr. Teller, illegally expelling Rafe, using unreasonable punishments on students who break the rules, and framing and unlawfully suspending the students of his class, and Hwang also plans to press charges and have Dwight and Stricker arrested. When Dwight puts his hat on, he realizes that it has green hair dye in it, though instead of being shocked, he accepts the joke this time. With Dwight and Stricker both terminated from Hills Village, Rafe is re-enrolled and Mr. Teller gets his job back.
After school, Jules soon arrives to pick up Rafe and Georgia, Bear also arrives in a taxi and is enraged that his car was partially damaged. Bear angrily lashes out at both Rafe and Georgia; however, Jules comes to their defense and dumps Bear for his abusive behavior. Bear storms away in a huff, and the family go home.
Rafe is later seen that night outside the school conversing with Leo, who tells him that since Rafe has now made friends with some of his classmates, he is no longer needed to fill that void. As Leo departs on a spaceship with aliens that Rafe has created in his earlier sketchbook, Rafe and Jeanne share a kiss, breaking rule #86 which is the final rule Rafe needed to break for an ends Justify the means deed.
The story ends with Leo, the two-headed dog, and a lot of monsters in the spaceship. Leo parties with the monsters, and Bear and Principal Dwight were in jail. Then the scene shows outer space, and the spaceship zooms off.
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Middle School: The worse years of my life
Saggisticat follows a middle school student who sets out to break every one of the many rules made by his domineering principal.