The students are at Kevin Stern's funeral after his scooter crashes through the window at a doughnut shop when Lily comes, on crutches due to her pelvis being broken and RJ has a choice to make. When Miles tells RJ to picture his life with Lily and then life with Jenny, he decides to tell Lily the truth about Jenny and him. Coach Sinclair holds a fundraiser to help fix the school bus that hit Lily. RJ is mad about this and holds a fundraiser of his own to help pay Lily's medical bills. Max, who wants to settle the score with Miles for beating Max's testicles repeatedly at the dance, cannot beat Miles publicly so Coach Sinclair signs both of them up for a sumo match. During the match, Miles gets the upper hand momentarily until Coach Sinclair trips Miles and Max finishes him off to win. RJ tells Lily that he took Jenny to the dance and that they kissed, and that he must take his shot with her. Lily, who is distraught by this, hits RJ with one of her crutches and declares that RJ is "dead to her" and storms out of the gym while wrecking the fundraiser booths. As they leave Miles tells RJ not to worry too much about Lily, and they both decide that RJ should focus on being with Jenny. In the end, Suzanne and Rick tell RJ that they are getting a divorce.
Cousin Vinny, RJ's cousin, comes to visit to help RJ and his mom move to a new apartment. Vinny later teaches RJ and Miles to look cool for girls. This helps RJ, who had asked Jenny to go out on a date earlier that week. Max hates the idea of Jenny going on a date with RJ and plans on making it as miserable as possible for Jenny and RJ. While at the restaurant, Vinny and Miles stay in the lobby while Jenny and RJ eat dinner. Max stops by and tells RJ and Jenny that this is his place and that they should leave. The last straw for RJ comes when Max throws a piece of bread into Jenny's soup and RJ stands up to Max and attempts to smooth things over with him. When Max tries to hit RJ, the restaurant manager (whom Miles, RJ and Vinny met earlier) knocks Max out and into a salad bar and tells Max and his buddies to lay off of RJ. Vinny and Miles come over and ask if Jenny and RJ want to leave. At the end of the episode RJ and Jenny kiss.
RJ and Jenny go to a lock-in at the school, where it is widely known amongst the students to be a "School Sponsored Orgy". Once there, Miles finds out that Lily plans to sabotage RJ and Jenny from sleeping with each other and Miles locks Lily in the bathroom to stop her. Afterwards, Miles distributes chocolate biscotti that he stole from his brother Chet to everyone but RJ, who is allergic to chocolate. Jenny and RJ sneak off to the Science Lab to be alone. Everyone in the gym who ate the biscotti starts to hallucinate since the biscotti is apparently laced with drugs from Afghanistan. Jenny, who is also affected, pulls off her panties and tries to give RJ oral pleasure but passes out instead. Everyone in the gym, including Coach Sinclair, starts to freak out from the drugs and attempts to flee the school but can't due to the doors being locked. RJ appears and opens the doors, letting everyone leave the school while he carries Jenny out and to the football field. As morning comes, Jenny wakes up on RJ's lap and he tells her what happened during the previous night. They leave the field with the sprinklers coming on and everyone else starts to recover from the drug-laced biscotti.
Jenny comes to school in a depression when she reveals that she has a zit, for the first time. Jenny is very upset about this after Miles tells her it wont go away in time for her cheerleader picture. Meanwhile, Lily gains a large sum of cash after her settlement money comes in from her accident, allowing her to buy her popularity from the jocks. This puts her at odds with RJ, while Miles ends up becoming her personal assistant. RJ tries his best to comfort Jenny with her zits, but ends up hurting her feelings. Lily comes to the realization that Robin is only using her to buy her expensive items like jewelry and make-up and finds Jenny in the bathroom sobbing to the fact that she has many more zits than before. Lily gains some sympathy for Jenny and tells RJ about Jenny and they come up with a plan to sneak her out of the school. Lily, Miles, RJ and Jenny grab the mascot costume and attempt to sneak out, Breakfast Club-esque style. Miles runs a diversion, leaving Jenny and RJ to sneak off to his house. While Jenny and RJ kill time there, Lily discovers Robin placed some cream in Jenny's make-up to give her zits. Lily hates this and places some of that cream in her make-up and gives it to the other cheerleaders, embarassing them completely for their cheerleading photo.
RJ's grade starts to suffer due to his life crumbling around him. Jenny tries to tell RJ that her parents are out of town for the weekend and says that she wants to lose her virginity then. Meanwhile, Miles gets into trouble with the hot substitute math teacher and has to stay after class. When RJ and his parents come to a parent teacher conference with Coach Sinclair, it is decided that RJ gets a tutor to help. RJ meets up with his tutor Amy and is shocked at how hot she is and fantasises about her. Amy calls her on it and he tells her what is happening in his life. Miles heads to the substitute's room and she ends up wanting to have sex with Miles. Stunned, Miles tells RJ the good news and has sex with her the next day in the janitor's closet. Jenny tries to tell RJ about the weekend then she meets Amy and leaves before she can. Amy asks RJ why Jenny is with him and he can't come up with an answer. Later on, Miles pulls a bug from his crotch and RJ tells him that it's a crab. In denial, Miles ends up grabbing another and admits that he does have crabs. Miles then comes to the conclusion that he will shave off his pubic hairs in order to have sex with the substitute again. He then vows not to have sex again and tells her that they are through. Jenny tries to ask Lily what it's like to have sex and Lily ends up telling her that she and RJ had sex. RJ tells Miles that he has doubt about him and Jenny but Miles reassures him. Lily comes up to RJ, telling him that she told Jenny about RJ and her. Jenny soon follows and Jenny says that RJ is not who she thought he was. Jenny leaves with RJ in a depression.
RJ's relationship with Jenny suffers when he is caught lying; Amy wants to help RJ save his father.
RJ tries to find a way to impress Amy and comes up with taking her to see Weezer, until they notice that the concert is for people over 21. RJ and Miles figure out that they need to make some fake ID's and get into the show that way.
RJ must choose between his mom and his dad when they both invite him to dinner on the eve of what would be their 20th anniversary. Elsewhere, Miles joins the cheerleading squad in an effort to get healthy.
RJ asks his dad for driving lessons as his 16th birthday approaches, but he gets more than he bargained for when his dad brings him to Hunkeez, a male strip club.
RJ throws a "Max Bash" to get back at Max Owens for ruining his birthday, and things quickly get out of hand when Max and his jock friends show up at the party.
RJ and Jenny get nominated for Mr. and Ms. Pinkerton right as he's ready to take his relationship with Amy to the next level.
RJ and Max Owens battle for the title of Mr. Pinkerton in the Season 2 finale. Meanwhile, RJ's relationship with Amy hangs in the balance.