High school mathlete Lindsay Weir rebels and begins hanging out with a crowd of burnouts (the "freaks"), while her brother Sam Weir navigates a different part of the social universe with his nerdy friends (the "geeks").
Lindsay's family and friends fear the worst when she quits the academic decathlon team and begins hanging around with a new crowd. A new friend tries to help her find her way. Meanwhile, Sam ponders asking cheerleader Cindy Sanders to the homecoming dance, while trying to cope with persistent teasing and torture at the hands of a savage bully.
Lindsay's friends learn that her parents are going away for the weekend and suggest having a kegger. Sam and Neal become worried after a school assembly focusing on alcohol-related deaths and they decide to switch the real beer with non-alcoholic beer. Daniel and Kim get back together and despite the lack of alcohol, the party quickly gets out of hand.
Sam convinces Bill and Neal to trick-or-treat on Halloween, but they end up embarrassed while Lindsay and her friends wreak havoc in the neighborhood.
Lindsay offers to help Daniel study for an algebra test, but ends up accused by the teacher of cheating. Daniel lends sexually naive Sam a porn film.
Lindsay encourages Nick to pursue a career in music. Nick continues to practice with his current band, but quickly decides he's better than them. Lindsay encourages Nick to audition for a bigger local band. When things don't go well in the audition, Lindsay is there to comfort Nick. After learning they have to shower in gym class, Sam, Bill, and Neal refuse to do it.
Sam, Neal, and Bill befriend a pretty new transfer student, but soon fear of losing her to the popular crowd and try to win her over with a series of fun things they plan for her. Lindsay, Nick, Daniel, and Ken decide to get fake IDs so they can see a hot local band perform at a bar. However, after they go through the trouble of getting their IDs and getting into the bar, the group is stunned to find out who the hot local bands lead singer is.
Lindsay reluctantly agrees to come over to Nick's house while his parents are out of town. Sam hopes to become lab partners with Cindy, but becomes jealous when Bill is named Cindy's lab partner.
Sam tries out to be the school mascot hoping to impress Cindy. Meanwhile, Daniel, Ken, and Kim suddenly become the basketball team's most rabid fans following a series of run-ins with jocks from the rival school, Lincoln High. Lindsay tries to figure out the best way to break up with Nick.
Lindsay's parents forbid her from hanging out with Kim, as they see her as a bad influence. Bill grows tired of being picked last for teams for baseball in P.E. class, and not being allowed to really participate.
A car accident results in Lindsay deciding to stop hanging out with her “freak” friends. She decides to rejoin the mathletes and start hanging out with Millie again. Sam adopts a new modern hair style in the hopes of impressing Cindy. When this fails, he seeks out a new wardrobe.
Neal learns his father is cheating on his mother. Ken develops a crush on the tuba player in the school's marching band and Lindsay helps set them up.
When Bill talks about being allergic to peanuts in class, Alan tries to prove he's lying but Bill ends up in the hospital after an allergic reaction. Lindsay smokes weed for the first time.
After fighting with his father, Nick moves out and to Lindsay's surprise begins staying with the Weir's. Cindy tells Bill that she has a crush on Sam. She asks Bill to convince Sam to invite her to a party.
Sam discovers that life as Cindy's boyfriend is not nearly as exciting as he had imagined. Ken's girlfriend ,Amy, confesses a shocking secret, putting Ken in an awkward situation. Lindsay struggles with asking Vice President George Bush a question during an assembly.
Daniel is sentenced to audio/visual class as punishment for attempting to pull the fire alarm to get out of taking a test. Lindsay is accepted to a two-week academic summit. Nick has a new girlfriend and takes up disco dancing.
Kim's friend, Karen, bullies Sam and calls him a geek. Kim invites Lindsay to dinner at her house, exposing Lindsay to the abuse Kim takes at home.
Lindsay tries to convince Harold to let her join her friends at a Who concert. Kim and Lindsay accidentally run over Millie's dog. Kim starts hanging out with Millie. Lindsay wants to tell Millie the truth about her dog, but Kim doesn't. Meanwhile, Nick teaches himself to play guitar and writes a love ballad for Lindsay and decides to play it for her despite Kens' objections. Ms. Haverchuck stuns Bill with the news that she has been dating Coach Fredricks.
Neal wrestles with the dilemma of whether to tell his mother about his father's affair. Lindsay is given detention after coming to the aid of a girl being attacked by a boy. Daniel deals with pressures at home and with Kim. He escapes from his problems through punk music.