It's the first day of a new school year. Brooke has self-image issues. Sam thinks Brooke is shallow. Josh tries out for a musical. Sugar raps. Nicole's picking a new cheerleader. Carmen and Mary Cherry apply. Lily won't dissect a frog.
Josh is pressured to quit the musical. Brooke comforts Carmen. Sam and her friends aren't invited to Glamazons' exclusive party. Sam and her dreamy teacher Luke have dinner. Lily still won't dissect a frog. Jane and Mike have big news.
Sam and Brooke clash over their first family dinner. Ms. Glass tries to make conscientious Lily cave in and dissect a frog. Josh's football coach and drama teacher clash over him. Sam's new editorial angers Nicole. The Novac is explained.
Josh has a spontaneous erection when Sam sits on his lap. Carmen accidentally sends everyone her e-mail about this embarrassing event. Harrison comforts hurt Brooke, while Sam and Josh bond. Lily's broke and finds a fast food job.
Brooke, Poppy, Mary Cherry, and Carmen are nominated for the Junior Court Homecoming Queen. Each runs a different style of campaign. Cherry's mom Cherry Cherry is introduced. Brooke and Sam can't stand living together.
Sam and Brooke bet on if Sam can land a boyfriend by the end of the week and if Brooke can prove that her relationship with Josh is more then just physical. Also, the gang plans to lose their virginity.
The students have to find nominees for Principal for the Day. While a custodial strike leaves the school a wild mess. Meanwhile, Brooke fears she may be pregnant, and Harrison has to deal with his mother being a lesbian.
"Popular" does Dickens' Christmas Carol. Everyone is invited to Sam and Brooke's first joint annual Christmas party. Carmen breaks her ankle and can't try out for Glamazons. For being a Grinch, Nicole's visited by the ghosts of Christmas.
Josh's father forbids him to do the musical. Sam and Brooke are asked by a network TV producer to make a video piece on Josh. Now that Carmen is a Glamazon, April Tuna becomes her obsessive fan. The Glamazons take a driving test.
Tensions between Sam's friends and Brooke's friends are leading to a rumble, but the guys intervene and lock the ladies in a school bathroom where secrets are revealed, new bonds are formed, and a friendship comes to and end.
School's dreamy new vice-principal Calvin Krupps attracts attention of several girls. Brooke tries to get Josh back. Harrison performs a song about Carmen's love life, which devastates her. Krupps gives his lazy students Tai chi lessons.
Harrison campaigns to save the job of the school's shop teacher when he puts his career in jeopardy by his announcement of plans for a sex-change operation. Meanwhile Cherry Cherry teaches a class at Kennedy High, Home Economics, to serve her community service.
Blonds and brunettes switch hair color to test Sam's natural selection theory that blonds always get preferential treatment. Bowling decides it. Losers get mohawks. Sugar falls for an Asian exchange student. Lily fails to save a lobster.
Lily and Carmen become Nicole and Mary Cherry's servants in hopes of receiving wigs to cover their mohawks. Sam and Brooke plan to stop their parents' wedding. Mary Cherry opposes her mom's decision to marry "CHiPs" actor Erik Estrada.
Sam tracks down Brooke's estranged mother and learns a lot about life from her. Brooke, Lily and Carmen try to cover for Sam. The boys use oblivious Mike to get into a strip club only to find Mary Cherry and Nicole stripping there.
The gang investigates the suspicious death of Ms. Glass in this season finale that parodies TV tropes that season finales often use such as murder, musical numbers, gore, nudity, teen pregnancy, terminal illness, wedding, earthquake, etc.