At the opening day of the new school year at Bayside, a flood of new transfer students from Valley comes to Bayside. They include prankster Ryan Parker, fame-seeking R.J. Collins, and Valley cheerleader Maria Lopez who are immediately at odds with Lindsey, Rachel and Tommy. Seeking popularity, Ryan schemes to make Maria the head cheerleader, R.J. the DJ for Bayside's radio and even asks Lindsey to the Welcome Back Dance while Tommy is trying to get back with her. But their feud threatens to engulf the whole school. Meanwhile, Mr. Belding asks Screech to hide cookies ...
Both Tommy and Ryan bug Lindsey's slumber party using a $1,000 communication set, that Screech bought, to find out which one of them she likes the best to go out with him to a rock concert. When Screech breaks the set, Lindsey discovers the microphone and decides to set up whoever planted the bug, while Screech tries to find a way to tell Mr. Belding about the set breaking.
Screech is assigned to teach drivers ed for the school. When Maria fails the class, she convinces a reluctant Screech to pass her so she can get a car for her 16th birthday. Meanwhile, Ryan, R.J. and Rachel plan to buy a car for themselves by scamming money from the school band, geeks and football hunks. They then must use the car they bought for the groups they scammed after Maria dents Mr. Belding's car while driving hers.
Rachel reluctantly agrees to tutor Bayside's football star in history and soon discovers that he is suffering from dyslexia, which enables him not to see letters clearly. Meanwhile, Lindsey and Maria compete all-out with each other to be elected Homecoming Queen, while Screech loses the homecoming crown.
During a weekend at the Palisade Hills mall, Ryan schemes to win Lindsey's affections by teaming with R.J. in a get-rich-quick scheme to sell students custom-made "Air Screech" athletic shoes from the sporting goods store where Mr. Belding and Screech work. The sneakers are a big hit, until Mr. Belding finds out and puts his foot down.
The gang goes for a week-long study program at California University where Ryan helps Screech become reacquainted with his old fraternity Sigma Alpha in order to make Screech feel better after his former frat mates don't seem to care about him. Meanwhile, Rachel and Maria find themselves being wooed by the same guy from the fraternity, and Tommy ends up getting hypnotized after attending a psychics class.
During a three-day weekend at the mall, Maria meets and befriends Justin Wells, a teenage film star who asks her to keep his identity a secret so he can have a normal weekend for himself. Meanwhile, Screech gets various jobs around the mall to get money to pay for a new bicycle after the prized one disappears from the sporting goods shop.
Not everyone is having a ball in Screech's school production of "Cinderella," because Lindsay becomes jealous when her Prince Charming, Ryan, lands the lead opposite Rachel. Meanwhile, Screech and Mr. Belding quarrel over how to direct the play.
The gang assembles a news magazine program for Baysides new cable-TV station. But after a disastrous start, Ryan and the gang fake several events to boost the ratings. Meanwhile, a phony Hollywood talent agent comes to the school to sign up R.J. for a chance in show business.
Ryan goes out on a date with Lindsey when he should be at home studying for an important physics test. So, he tricks Screech into having a fire drill so he can avoid taking the test. But Screech turns on the sprinkler system which ruins the homecoming float the gang builds. When the gang and Mr. Belding find out that Ryan was responsible for the disaster, they all join forces to get back at him in a very cruel way.
The Bayside Junior Prom arrives and Mr. Belding puts Screech in charge to reduce budget costs. Lindsey is asked to the prom by both Tommy and Ryan. So she must make a choice that will affect both of them. Meanwhile, R.J. asks the attractive Valerie to the prom, but her wary big brother warns R.J. not to touch her, and Rachel is depressed that no guy has asked her to the prom.
After Tommy D falls for Nicole, a highly refined new classmate who is the new ballerina of Baysides ballet club, Ryan tutors him on the finer points of cultural comportment in hopes that Tommy romancing Nicole will lead to her wealthy father getting him, R.J. and Maria tickets for a MTV rock concert. Meanwhile, Screech mistakenly thinks Mr. Belding is dying after overhearing his phone conversation about increasing the amount of his life insurance policy.
A ankle injury during gymnastics practice on the uneven bars sidelines Lindsay and leaves her fearful to compete with the other girls. Meanwhile, Tommy becomes the water boy of the team after losing a bet with Rachel, and Ryan tries to make more people come to the gymnastics meet to keep it from going under by fabricating a story about Michael Jordan will be attending the gymnastics event at Bayside.
Ryan secretly works behind everyone to get Tommy selected as principal during Student Teacher Week so that the gang can slack off by turning the school gym into a Bed and Breakfast for foreign tourists. Meanwhile, Rachel becomes the music teacher and has problems with the class slacking off than practicing for an important music concert.
Screech tries his luck at winning the lottery and the combination of his birthday and Mr. Belding's looks like that he won $2 million. Screech then lets the thought of wealth go to his head while the gang plans to uses his money to rent out the gym as an exercise place to make more money for themselves.
At the Palisdes Mall, Rachel feels like she's the odd girl out when Lindsay starts getting real chummy with Maria. Meanwhile, Ryan gets a job at Mr. Belding and Screech's candy store so he can enter a shopping spree contest the mall is giving.
The gang goes to Screech's grandfather Eddie Powers Sleepy Mountain Ski Lodge for the Christmas holiday. With business slow and no snow on the ground, the gang becomes his volunteer staff, while Ryan plans to keep the guests there at any cost. Meanwhile, Lindsey's attraction to the young kitchen chef, Greg, cause her and Ryan to break up for good.
Mr. Belding, Screech and the gang set sail for two months of ocean-going course work at sea on the S.S. Morning Star for the summer, where the gang proceeds to go overboard with slacking off than go to biology class. Meanwhile, R.J. meets Carla, a disabled girl in a wheelchair whom he regrets about asking her to the ship's dance.
On the S.S. Morning Star, the gang bets they can make enough money to buy Mr. Belding a birthday present, if they score some fake ID's to get them into the ship casino. But when they do get in, greed takes over when Ryan loses all of the gang's money and he must think of something before Belding and the rest of the gang find out.
On the last week on the S.S. Morning Star, Screech gets depressed after receiving a break-up letter from his girlfriend, Alison. The gang tries to cheer up Screech by setting him up with a beautiful German model, who turns out to be a gold digger plotting to marry him in order to get her Green Card.
At the Palisdes Mall, Lindsay takes up smoking, while Tommy tries to quit his own habit. When Ryan tries to warn Lindsay of the dangers of smoking cigarettes, she thinks he's just blowing smoke... like her. Meanwhile, Screech tries to boost business for the candy store during Mall Mania weekend by selling trick candy which Mr. Belding disapproves.
At the Sleepy Mountain Ski Lodge, Ryan has spent the whole week in his room brooding over his breakup with Lindsey who dumped him for the hotel chief Greg. However, Ryan tries to get back at Lindsey by trying to make her jealous when he brings another girl to show off to her. But the plan misfires with the rest of the gang caught in the middle while they are preparing to throw a birthday party for R.J. on the 21st. Meanwhile, Screech and Mr. Belding go on a overnight camping trip in the woods to be accepted into Eddie's Spotted Owl Men's Club.
On Christmas Eve, Screech tries to prevent Mr. Belding from leaving the ski lodge after he invites Mrs. Belding to meet him for a surprise visit. Meanwhile, Tommy tries to help the new employee, Robin, by making her the head waitress so she can get all the tips to help her needy family.
Screech is having trouble coming up with a New Year's resolution so the gang tries to help him out by sharing their own New Year's resolutions as told through a series of flashbacks from episodes of the past season.