Todd gets transferred to Wayside School, a school that was accidentally stacked 30 stories high instead of 30 rooms sideways. He is assigned tries to Mrs. Jewls' class on the 30th floor, where he attempts to fit in with the class, usually with mixed results. However, due to his failure to cope with the school's unorthodox system of learning, Mrs. Jewls writes his name on the chalkboard and puts a check mark next to it.

The teacher threatens that he will be sent home on the kindergarten bus. The class is about to be crushed by the trash compactor that was accidentally on the 30th floor and the machine would work every time the PA comes on, Todd's outbursts start, and Mrs. Jewls writes his name under the word "discipline" and sends him home on the kindergarten bus.

Mrs. Jewls and her class play dodgeball, and Principal Kidswatter tags Todd and is finally tagged. Mrs. Jewls pronounces Dana as class president. While Todd is sent home again on the kindergarten bus after he does more outbursts to Mrs. Jewls, the trash compactor is on again. Dana cries and tells Mrs. Jewls that she herself is the worst class president. Todd, however, has snuck outside Mrs. Jewls' classroom, and tells Maurecia and Mrs. Jewls and the students that he has to get them out.

"Pull My Pigtail": It's Valentine's Day at Wayside School and Dana attempts to force Todd to fall in love with Maurecia by making him pull her ponytail. Meanwhile, Principal Kidswatter thinks Myron is his guardian angel.

"Meet the Pets": After Todd tells how he has once lost a goldfish named King Arthur, everyone brings their pets into school and Todd must watch them so that he'd learn to be more "responsible". However, when the pets escape and run all over the school, Todd will need some help from his friends. Todd finally brings a new live fish named King Arthur the Second.

"Honors Class": Maurecia is promoted to the Honors Class instead of Dana. Now she must "escape" it at all costs, while Dana tries to enter. In the end, we find out Mrs. Jewls' class is actually double Honors Class.

"Mascot Madness": The tetherball team kids want Todd to be the new mascot so that they can finally win some games, but Todd does not want to, so Dana creates a giant version of his head for Myron to wear, and he becomes "Big-Head Todd".

"Best Friendzzz": Myron and Dana have been best friends for a long time but one day after a falling out occurs between them, they decide not to be best friends anymore. So Myron becomes Shari's new best friend (although she is asleep, but uses a glass to hear what she's thinking) and Dana becomes Todd's new best friend. Meanwhile, Mr. Kidswatter tries to ease his stress with a new machine, called "The Wizomatic 3000", he bought for $19.99. At the end, Myron and Dana reconcile and become best friends again, and Todd tries Myron's brain-listening glass trick on Shari (only to find out it truly does work as he hears horses, pinball, and karate).

"Myron vs. Normy": In order to avoid getting in trouble, Myron pretends to be Normy, his made up twin brother. When he returns to the class, everyone thinks he is cool (and in Dana's case, sweet and cute) and they want him to be class president. However, Todd (and Shari) can see right through "Normy", and Todd tries to get Myron to tell everybody it is really him.

"Channel Kidswatter": Principal Kidswatter wants to run a home-shopping channel out of his office, and gets the students to supply his cheesy inventory of trinkets under the guise of a new "arts" curriculum. Todd tries to prevent it from happening, but then works for it. So it's up to Maurecia and Jenny to stop the home-shopping channel.

"Mad Hot": Principal Kidswatter challenges another school for the annual Wayside dance competition. He then picks a random team, consisting of Todd, Maurecia, Dana and Myron.

"Principles of Principals": Todd enters the Principal for a day contest and wins. No one else has entered it because it is a trap, as the winner has to do everything on Kidswatter's super-long list. Todd decides to complete the list, and improve the school all in one day.

"Rat in Shining Armor": It's the spring Halloween dance and everyone must dress up as something. Maurecia wants Todd to dance with her until Todd finally says no (because he got bounced half way across the room from her punch and he needed a break) and points out the fact that they're not going out after Maurecia thinks he wants to break up with her making her run away, crying. Feeling bad for Maurecia, Miss Mush puts her dead rat in an old knight suit so Maurecia has someone to dance with making Todd jealous. Todd finds out that it's Miss Mush's dead rat in the suit, so he exchanges costumes with him so Maurecia won't be heartbroken when she finds out.

"Todd Falls in Love": Todd arrives at school and finds out Maurecia has posted pictures of love posters about Todd all over the school. Todd decides he would do anything to prove that he will not be her boyfriend, so he eats Mush's mushroom surprise, that makes him fall in love with Mrs. Jewls. Maurecia finds out and tries to get Todd to like her again.

"Music Lessons": Myron discovers a strange nose flute called the Strumplefloozle, and uses it to control his friends. However, it also makes cows tear down the school.

"My Partner Gets All the Credit": Maurecia is paired with Myron in the Wayside Games, and since Myron is not a good athlete, she must do all of the work. However, every time she wins an event, Myron gets the credit, and Maurecia is starting to get angry with Myron.

"Louis Gets Some Class": Kidswatter finds out that Louis never passed his final exam, and sends him back to class. Myron gets upset that Louis is more popular than he is. Mr. K than calls in Mr. Osteo to give Louis his final exam. Later Myron finds out that Louis did indeed graduate, as he found his real folder when he was in Mr. Kidswatter's filing cabinet. Mr. K says "Let me see this real folder" and Myron was right. Louis DID graduate.

"Dana Checks Out": When Dana is tired of organizing the class, Jenny lets her use her bike to see all 30 floors of Wayside, including the non-existent 19th floor. After Myron ruins the class, they must get Dana back. But before Dana rides into the 19th floor's boarded up room, Jenny was able to talk Dana out of it by revealing there was a good reason she's never seen the 19th floor. When Dana bumps Jenny's bike onto the ramp, it comes back, only with the seat signed by Mrs. Zarves.

"Kidswatter: The Movie": The kids are assigned to make a movie about Principal Kidswatter for the new movie making class, and Todd is cast in the lead role. However, he soon becomes even worse (if not just as bad) than the real Kidswatter. Todd, through tears in his eyes, says that his success has become a failure, but Myron interrupts, saying he could use that in the movie, only with more feeling. The class watches the Kidswatter movie, and after the ending, tears are in Kidswatter's eyes.

"Be True to Your Elf": After Kidswatter says he can't lead the parade (on account that his costume looks to similar to the leprechaun he encountered before), Stephen tries to be "Mr. Normal" so he can lead the school parade.

"Oh, Brother": Goon, Dana's older brother, visits and Myron wants to be a rebel just like him, but he's not a rebel. Mrs. Jewls and Kidswatter try to capture him. Mrs. Jewls tells Todd, Maurecia, and Dana that Goon is a fugitive. Meanwhile, Todd and friends save Goon from being captured.

"The Rat Truth": Sammy is terribly sick (but dead) so Miss Mush randomly asks Dana to watch him while she goes on a hunt for the golden pot of Mamaland that makes food to cure the sick. Sammy becomes a truth stick in Mrs. Jewls's class and is feeding words into his mouth. Later, Sammy is kidnapped by Mr. Kidswatter.

"Extra Curricular Riddicular": All the kids are forming bizarre after-school clubs, except for Todd, who creates a "Science Club". Myron laughs at him (only because he doesn't have a club), believing his club will be better, until he sees Todd's club has managed to build a functioning rocket. Jealous Myron tries to form a science club and build a rocket of his own. Myron accidentally launches the rocket Kidswatter is in and makes Todd cry. Todd wants to confront Myron, until Dana stops both of them from ruining more of their friendship.

"Le Race": Ever since Kidswatter fired Le Chef, he has been trying to get revenge on Kidswatter. One day, Myron receives a note saying Kidswatter is to be challenged to a game of Parkour with the chef. Can Kidswatter beat this match before Le Chef takes over the school?

"Kidswatter's Opus": Mrs. Jewls is sick. So the kids need a substitute. Unfortunately, all substitutes aren't available so Kidswatter has to step in as a substitute and teach everyone stuff the Kidswatter way.

"Miss Fortune": It's a regular day at Wayside. Miss Mush suddenly asks Myron, Dana, Maurecia and Todd about their future careers. She makes bowls of Mushroom Surprise that tell the future at the bottom. Meanwhile, Kidswatter sees his future from the last time he ate Mushroom Surprise and wants to change it.

"Myth of Nick": After hearing too many myths of a kid named Nick, Todd wants to take rid of them. He learns all of "Nick's" old tricks. Telling Maurecia, Dana, and Myron about the fake myths, Todd, with a snorkel over his mouth, dives in a can of beans, and comes out, speaking in a muffled voice. Meanwhile, Todd knows and tells the class that "Nick", who is Louis, exists.

"Slow Mo Mo": Maurecia loves being fast and first because of her wheels on her roller skates. But one day when Maurecia and Principal Kidswatter bump into each other (because of Maurecia's wheels), Kidswatter bans all round things from Wayside School including Maurecia's wheels and everything round becomes squared. She hates it because she is last, slow and late for everything. Kidswatter tries again and makes everything squared become round again. Meanwhile, Todd, Dana, and Myron join Maurecia.

"Upside Down John": It's the 30th floor science fair today and John is showing his science volcano. However, he hates how it turned out. John then starts to think this is so because he does everything upside down. So, Todd, Myron, Dana and Maurecia try to help crying John get right-side up, just like the kids who are parallel and are upside down. In the end, Mrs. Jewls tells John, without the help from Todd, Maurecia, Dana, and Myron, that being upside down is not a bad thing. Meanwhile, Kidswatter is doing an I.Q. test to see if he is smart.