The episode covers the boys' first day of fourth grade. The three previous seasons of the program featured the main characters in the 3rd grade with Mr. Garrison in the role of teacher. This grade-change plot device allowed the writers to introduce a new teacher, Ms. Choksondik, and also make a new opening sequence in which the show was said to be "Faster", have "more explosions" and that "You love it".
This episode marked the boys' move into the fourth grade. Not knowing their new teacher (aside from the fact that it's woman from Denver), the boys plan to exert dominance over the teacher. Before the beginning of class, Stan comes up with an idea: at 8:35am, everyone jumps up on their desks, pull down their pants, and shout "Kiss my ass!" After meeting their new teacher, Ms. Choksondik, she explains that fourth grade will be different and the children are all very frightened. Cartman alone stands up and pulls down his pants, very annoyed no one else followed the plan. Ms. Choksondik is depicted as a middle-aged woman with disgustingly saggy, pendulous breasts that she neither notices nor is ashamed of. In an ironic twist, none of the children notice her obscene-sounding name (which is pronounced like "chokes on dick"); instead, they come up with their own insulting nicknames (such as "makes me sick"). Cartman eventually makes the children realize that they took the ease of the 3rd grade for granted and do not want to go through a whole year in 4th grade. They seek help from two scientific Trekkies and ask them to create a time machine so they can return to the 3rd grade. The Star Trek fans then construct the device using Timmy's wheelchair.
Meanwhile, it is revealed that the teachers do not like Ms. Choksondik any more than the students do, especially as when she lifts her arms up, a small section of her breasts come into view, which Chef finds freaky. Ms. Choksondik reports to Principal Victoria, Mr. Mackey and Chef that she is unable to teach the children in her class and attempts to speak to Mr. Garrison (who was fired after "Cartman Joins NAMBLA" after he was accused of trying to solicit sex from Cartman), but she is unable to get any information. The next day in class, the children begin their plan of traveling back to 3rd grade. However, the plan backfires and instead of creating a portal back in time, Timmy is driven through the classroom wall in his uncontrollable wheelchair. He is unable to stop the wheelchair as it would explode if he slows down or if he gets off (a reference to the film Speed), because of the materials used to convert it to a "time-travel" device. Kenny is dragged to death in an attempt to disarm the device, after which Stan replies "Well who didn't see that coming?" (this is one of the few episodes were Kenny's death gag is referenced by one of the characters). Eventually, a portal does open and Timmy is thrown into the pre-historic past.
Ms. Choksondik goes on a journey to find Mr. Garrison in order to learn how he dealt with the class, who has gone into a self-imposed exile in the mountains after his romance novel won the Gay Pulitzer Prize award. Mr. Garrison agrees to help her, and shows her how he does it. Eventually, he then comes to the realization that he needs to admit and confront his "gay side" (in a parody of Luke Skywalker confronting his dark-side in The Empire Strikes Back). The children try to convince the two Star Trek geeks to build another time machine but they refuse to work together because of a disagreement over how many original Star Trek episodes were made.
The arguments are notably inconsistent; the fan wearing green says there are 72 and not 73 and then claims the opposite minutes later. His friend starts out claiming that there are 73, then goes back to 72, then claims 73 yet again. All of these are incorrect, however, because there are, in actuality, 79 episodes of Star Trek: The Original Series.
In the end, Ms. Choksondik uses Garrison's methods to gain the class' attention, explaining how pointless it is to go back in time to relive the good moments as there many new challenges to face with in life. Realizing that Ms. Choksondik is right, they also realize that 3rd-grade was never as great as they remembered it to be, and get mad at Cartman for making them think 3rd-grade was so great. They decided to accept the 4th grade as it should be, much to Ms. Choksondik's relief. Timmy comes back with "souvenirs" from the eras he had visited. Mr. Garrison openly admits his homosexuality to Principal Victoria, Chef, and Mr. Mackey, and asks for his job back. They reply with "I'm sorry, we don't hire gay people," and laugh derisively.