On the first day of the new school year at Bayside, Screech Powers returns as Mr. Belding's administrative assistant for a project he has with CU, and he quickly drives Mr. Belding up the wall with his bumbling ways while Mr. Belding has problems with his new office, complete with high-tech gadgets. Meanwhile, Brian Keller, a new transfer student from Switzerland, peruses Rachel Meyers, who accidentally ruins her mother's $700 suit jacket meaning the gang must come up with a plan to pay for a new jacket, so they plan to throw a party at Bobby Wilson's house, the new ...
Mr. Belding and Screech get jobs as summer managers at the Palisade Hills Country Club owned by Ed Harrington, an old friend of Mr. Belding. Screech makes the mistake of hiring the entire gang as club staff who immediately get into trouble when they dent Harrington's car. Meanwhile, Harrington's attractive daughter, Alison, falls for Screech. When a freezer containing food breaks down before a Western-themed barbecue, the gang saves Mr. Belding from being fired by throwing a luau themed party instead.
Megan's running the school blood drive this year, but no one shows up to donate any blood, and Screech falls for the blood drive nurse Penny Brady. Meanwhile, the gang must find a chaperon for their hiking trip and Brian thinks that Screech will do. So, Brian schemes for Nurse Brady to go out on a date with Screech in hopes that he will go on the camping trip, while Mr. Belding tries to get in shape after learning of his high cholesterol level in his blood.
The gang is competing for best booth at the annual Bayside Carnival. Brian and Rachel decide to hold a dunk booth while Lindsay and Tommy have conflicting emotions about running a kissing booth. Meanwhile, Bobby is threatened by a bully, named Kirk, who wants Megan. So, Bobby gets karate lessons from Screech.
At the Palisade Hills Country Club, Brian becomes frustrated at Rachel's pinning for her boyfriend. So, with Screech's help, Bobby decides to try to make Rachel jealous by hanging out with an attractive tennis instructor. But Brian doesn't expect the instructor to fall for him. Meanwhile, the gang competes in a July 4th "tipathon," a contest where the person with the most tips will double his or her earnings.
When the faculty advisor for the school paper quits, Screech lobbies for the job and gets it, so he drafts the gang to do the paper with him and they come across a hot story involving the football coach giving more financial funds for the football team than the girls swim team. But another issue soon arrives: is the writing paper more important than the gang's performance on the PSAT's?
Rachel's college boyfriend, David, unexpectedly arrives at Palisade Hills for her birthday party which means she must make a choice to which one she wants to be with: him or Brian. Meanwhile, Screech decides to make a promotional video for the Country Club.
When the Palisades Country Club holds it's annual Charity Auction and Picnic, the male staff get auctioned to various women bidders to compete in various events, and the winner gets a hot air balloon ride. Screech gets jealous when Alison "buys" Brian, Megan gets stuck with Bobby, and Rachel ends up buying a nerd. Screech becomes jealous when Alison is teamed with Brian, while Tommy D tries to avoid winning the contest with Lindsay because he is afraid of heights. So, Tommy tries rigging all of Bobby's events, but as usual, everything turns out the wrong way for Tommy.
Bobby tries to get new members to join Baysides Glee Club, but doesn't have much success until the girls see the new hunk music teacher and all compete to win his affections. Meanwhile, Brian decides to join the Glee Club to be near Rachel, but he has no talent in singing so he asks Tommy, who turns out to have a great singing voice, to lip syn-ch for him, while Mr. Belding tries to prevent budget cuts from ending the Glee Club's run.
Palisade Hills holds it's annual Christmas In July party, and Screech is worried about what to give Alison in a gift exchange. Bobby is worried about what to get Mr. Harrington, and Tommy worries about his present for Mr. Belding. Meanwhile, Megan protests the swimsuit portion of the Miss Snow Queen pageant.
While Tommy, Lindsey, Bobby, Brian and the rest of the school get into spirit for Bayside's annual football game with Valley High, tensions are high when Megan begins dating a new guy, named Doug Parker, whom is the captain of Valley's football team. As a result of this 'Romeo and Juliet-type' romance, the whole gang joins forces to try to break them up, as well as try to steal Doug's football play book so Bayside's team can win.
The summer at Palisade Hills Country Club is over and it's time for the farewell formal dance. Rachel is sad to go, Megan doesn't have a date, Bobby want's a date so bad with a rich club member that he is willing to lie about being wealthy to get her. Meanwhile, Screech agonizes over Alison's acceptance to Gilliards School of Music in New York City and they must bid each other a proper farewell.
In this episode that tackles the sensitive subject of anorexia nervosa, Lindsey becomes obsessed with losing weight in preparation when a local TV show, called "Club Jam" which will hold a dance contest at Bayside. Brian asks Rachel to be his dancing partner, while Bobby and Brian trick Megan's partner, Kent, to drop her so Bobby can go with Megan. But Bobby secretly reveals to Megan that he doesn't know how to dance.
Mr. Belding treats the gang to a week-long trip to Gold Canyon Ranch, a dude ranch owned by Screech's Uncle Lester and his bullying son Clint. While Mr. Belding and Uncle Lester are away, the gang gets into trouble in the hills looking for gold.
While Uncle Lester and Clint are away, Screech is put in charge of the dude ranch which leads to a quarrel between him and Mr. Belding over planing a square dance. Meanwhile, the gang looks to play poker with two strangers, named Bo and Travis, who appear to be easy marks. But who actually are a couple of clever con men, in which one of whom woos Megan to learn the gang's poker plans.
Lindsay can't afford to get Tommy a birthday gift, so Brian and Bobby help her out by hijacking the school video project so she can do a video about Tommy. But their plan hits a snag when Brian's younger sister, Katie, and Tommy fall for each other, causing Lindsay and Tommy to break up for good.
It is the year 2020 and the graduating class of Bayside High sits in Principal Belding's office with an old Mr. Belding as they open a time capsule left behind by Bayside's graduating class of 1995. All time capsule stories from the Class of 1995 are told via flashbacks using clips from previous episodes (mostly from Season 2).
During a break in the school year, Mr. Belding takes Screech, the gang and some of the school members on a week-long school sponsored ski trip, but problems ensue with Brian's lack of attention to Rachel and Lindsay's attraction to a college boy named Chris, which prompt the girls to go to a frat party where Lindsay and Tommy have too much to drink and the results are Lindsay getting sick and Tommy breaking his leg after getting into an accident.
On the last day at the ski lodge, everything is perfect until Tommy (still incapacitated by his broken leg) and Megan to go out on a date, sparking hard feelings with Lindsay, Bobby, Rachel and even the neutral Brian who gets caught in the middle. Meanwhile, Screech doesn't know what he's getting himself into when he agrees to model for a thoughtless ski designer named Ramon-Ramon.
Rachel learns that she won't be able to go to Bayside's Annual Dance Ball unless she gets a 'C' in a history midterm, which leaves Brian in a dilemma when he sees a copy of the midterm and is tempted to give the answers to her, but it leaves Megan suspicious to how Rachel passed the test 100% which leaves Brian guilt-ridden. Meanwhile, Screech enlists the help of Bobby, Tommy, and Lindsay to help him impress Mr. Belding who must write an evaluation of Screech's work at Bayside for CU.
Tommy D takes a job as an auto mechanic and enjoys his job so much that it interferes with his school work. So he decides to drop out which disappoints his father, Mr. Belding, and the gang. So, Screech decides to step in to make Tommy realizes how difficult it is living on his own.
On Bayside's 40th anniversary, Rachel is running for Prom Queen and Bobby is running for Prom King. But everyone's plans are soon sidetracked when a wealthy industrialist and former alumni from Bayside, named Mr. McMillian, arrives when he decides to buy the school from the school board with the intention to demolish Bayside, meaning that the gang will be broken up and sent to other schools... including the hated Valley High.
Screech is supposed to mail Mr. Belding's application to join a well-known community of principals. But when Screech misses the deadline, he convinces Mr. Belding that he's been accepted to the society anyway: a scheme involving James the actor. Meanwhile, the gang tries to buy the Max's one millionth burger to win tickets for the MTV music awards.
After finding out that McMillian had one girlfriend when he himself was a student at Bayside in 1959, Mr. Belding, Screech and the gang attempt to track her down in hopes that she will talk him out of demolishing Bayside. At Bayside's 1950's nostalgic prom, news of Bayside's immediate demise draws some of Bayside best known alumni, Zack, Lisa and even A.C. Slater, to help the new gang save the school.