At the funeral for Kevin Stern, Lily Miran reveals that she has survived both the bus accident, and her night with RJ, who continues to find himself torn between his desire for Jenny Swanson and Lily's seemingly undying love/lust for him, all while Pinkerton High tries to raise funds for a new bus and he tries to raise funds for her treatment. Meanwhile, it is becoming clear that the Berger family trait isn't doing enough to keep his parents together.
It's "Lock-In Night" at Pinkerton High, and RJ tries to use it for the opportunity to finally have sex with Jenny, but a bitter Lily Miran will do everything she can to make sure that doesn't happen. Miles brings biscottis made by his brother Chet to the lock-in which makes makes him the life of the party. Unfortunatley, they're laced with something that gives the party more life than the kids can handle.
Thanks to a settlement by the local school district, Lily not only gets successful medical treatment but a new makeover that gets her in with the popular crowd at Pinkerton High. Meanwhile, Jenny suffers through a mysterious sudden outbreak of severe acne just before an upcoming photoshoot of the cheerleaders and is embarrassed to be seen in public, despite RJ's efforts to comfort through the ordeal. Is this just natural teenage hormones, or does someone have it in for RJ's girlfriend?
When the pressures of his parents divorce and his overall school life begins to send RJ's GPA down the toilet, Pinkerton High assigns a tutor to him named Amy Bresner, who apparently has taken quite a shine to him. As Jenny seeks to lose her virginity to RJ, Lily reveals that she had him first, which makes her wonder if he's after his new tutor. Miles seems to be getting lucky himself, when he loses his virginity to a horny teacher, who unfortunately gives him crabs.
RJ seeks advice from his dad, but Rick is obsessed with his Dream Board. Amy symphatizes with RJ and decides to help with Rick. Miles goes cluelessly into a peer support group after a girl, only to find that Lily is already taking part.
Coach presents RJ a bargain: RJ helps him with Ms. Berger, he helps RJ with Amy. RJ decides to ask Amy to Weezer's concert, but it is for 21 and over, so RJ has to accept the bargain. Meanwhile, Lily and Hamilton's romance is blooming.
R.J. has to juggle his parents' 20th Anniversary, the first one they spend separated, both of whom drown their sorrows in alcohol. Amy offers to help him keep his parents from coming apart, but neither his mom, nor Coach Sinclair make it any less difficult. In an effort to get in shape, Miles tries out for the cheerleading squad, and surprisingly the mishaps during practice aren't caused by him.
On the verge of his 16th birthday, RJ wants to learn to drive, and out of desperation asks his father for help. The vehicle he trains in however, is sponsored by a job that his old man had a long time ago... a male strip club franchise! Meanwhile, as Jenny recovers from her cheerleading "accident," she and Lily become closer to each other, and she invites the former head cheerleader over to a slumber party at her house where they bond over their hatred of Robin Pretnar.
RJ finally turns sixteen, and Amy promises to give him a "birthday surprise," but only if she stands up to Max Owens. And he does so in a big way by inviting everyone who has ever been bullied by Max over to his sixteenth birthday party at his father's motel room.
Now that RJ knows Max's secret, will he use it? Getting Amy back is, after all, more important. And can he help his dad win his mom back? What are Jenny and Lily planning together? Will there be Mr. & Mrs. Pinkerton or Ms. & Ms. Pinkerton?