Emily has been accepted to the prestigious Cousteau Institute in France, but does not want to attend because she and Brandon are in love. Brandon observes her passion for marine biology and encourages her to pursue her dream. Brenda balks when she is asked to appear nude in an experimental campus play. The frat and sorority pledges must endure a series of humiliating experiences during "Hell Week." The upperclassmen order Steve to steal a prize autographed baseball from Professor Randall for a scavenger hunt, but he gets caught. Andrea breaks up with Dan and begins dating Jesse. She learns that he is a UCLA law student who attended undergraduate courses at Yale.

David's work and study schedule begins to take a toll on him when mid terms come around, leading him to start using crystal meth. His erratic behaviour worries Donna and Kelly. Dylan wants to help Suzanne with her financial troubles by giving her $10 000 but Jim urges Dylan to let him do a background check on her first. Steve decides to take his suspicions about John Sears to their fraternity chapter president. Brandon continues to tutor D'Shawn in sociology but still feels that Professor Randall is giving him preferential treatment. During a basketball game, D'Shawn sustains an injury that he fears will impact his future career prospects. Andrea learns from her new RA that Dan Rubin has transferred to another dormitory.

Lucinda temporally loses interest in Brandon when she flirts with Dylan to ask him to finance her documentary film. Meanwhile, Kelly and Brandon spend the weekend together at a task force retreat where they meet the university Chancellor, Milton Arnold, Dean Trimble and the Chancellor's teenage daughter Clare, where Brandon and Kelly become more attracted to each other and brush off Josh who's still hounding them. Brenda and Donna befriend a stray dog that escapes from the university's lab, whom they name Rocky. Also, Andrea discovers that Steve is allowing Muntz and his frat buddies to use her dorm room for nooners. Andrea protests, but changes her mind when Steve begins to date her dorm resident advisor, Kathy Fisher.

In the two-part season finale, Brandon goes to Washington D.C. as a part of the college task force to meet the president. Kelly follows Brandon to Washington to get him out of a jam when Clare and Lucinda arrive at the hotel to pursue him. At the CU Mardi Gras, David impresses pop star Kenneth "Babyface" Edmunds, and his recording manager Ariel with his keyboard music and Donna catches David in a very compromising position with Ariel. Steve runs into Celeste who's now with John Sears. Kevin and Suzanne get married in a semi-formal ceremony where he persuades Dylan to cut out any outside investment in their business offer. Jim becomes angry at Dylan for making such a rash move and Dylan fires Jim as his financial holder. Dylan then goes to a bank and gives Kevin full power-of-attorney control over his money, unaware that Kevin and Suzanne have had a hidden agenda for Dylan's inheritance all this time. After her major success in the CU play, Brenda gets a scholarship offer to study acting in London and she pays a visit to Dylan's place before leaving. Also, Andrea and Jesse experience the joys and fears of parenthood after their daughter is born.

Brandon has trouble coping with Josh's sudden death in a car accident, which is a challenge to his political position when he's forced to fill Josh's shoes. Meanwhile, Donna finds a new man for herself, a KEG member named Griffin Stone, who her mother wants her to date. David meets Clare for the first time, and they, too, become close. Also, Valerie continues pursuing Dylan, who lays out ground rules that their clandestine relationship is based purely on sex, while Valerie continues her "good girl" charade in front of Steve and everyone else.

Kelly's senses alert her to be suspicious of Valerie's true unwholesome colors when she catches her smoking pot and she naturally makes a big fuss about it. But to Kelly's surprise, she cannot get a sympathetic ear. Steve refuses to believe Kelly, thinking that she's just jealous. Even Brandon is skeptic and tells Kelly to give Valerie the benefit of a doubt. However, Donna doesn't seem to care and tells Kelly that what Valerie does in her spare time is none of their business. Later when Kelly sees Valerie at the Peach Pit drinking and flirting with Dylan, she immediately tells Steve. But when then both confront her, Valerie (a true master of manipulation) convinces Steve (but not Kelly) that it was Dylan who made a pass at HER. All in the meantime, Valerie begins to grow suspicions of Dylan's cash-flow state when she discovers him stealing money from the Peach Pit to support himself. Meanwhile, Steve decides to revitalize the Peach Pit by throwing a rave party to boost business. While working on a video project with David and Clare, Donna meets a musician and carpenter named Ray Pruit. Also, Andrea juggles college and child care.

Brandon, now the new student body president of CU, has his first challenge when he is pressed into action by some human-rights activist students who are against the chancellor's friend Quintaro, a visiting Asian dignitary from a fictitious South-East Asian country of Selanesia, who is accused of human-rights violations which puts Brandon at odds with both Clare and Chancellor Arnold. Meanwhile, Valerie helps Steve, Kelly, and fellow KEG members Griffin and Muntz, plan the theft of a rival college's mascot, a huge stuffed bear, during homecoming weekend. Donna skips the caper to spend some time with Ray at his family's pumpkin stand. Also, Andrea is depressed when Jesse is spending more time studying and bar tending than being with her. Andrea then meets a mysterious guy, named Peter, at her local laundromat. Elsewhere, Dylan forces Valerie to keep his financial situation a secret. But when Valerie later walks in on Dylan cheating on her with a local prostitute, she vows revenge.

When Dylan is put in a coma after a car accident while driving under the influence of heroin, bizarre near-death dreams he has mirror his fight for life which involve his drug dealer, his high school principal Mrs. Teasley, Kevin, Suzanne, Erica, Valerie, the Walshes, and his own long-dead father, Jack. Meanwhile, Steve is bothered by the appearance of his annoying and overbearing father, Rush, at a flag-football tournament as part of the KEG sports weekend.

Brandon and Dean Trimble are caught in the middle of a conflict when several Jewish students, including Andrea, protest the scheduled campus appearance of a controversial, anti-Semitist, African-American orator, in which the demonstrations and near-riots disrupt Kelly's photo shoot for the magazine. Meanwhile, Donna plans a party for Ray's 25th birthday. In the hospital, Dylan spends the time talking with his mother Iris, while his drug dealer pays an unexpected visit and threatens him not to tell the police about their business.

Emily flies back from Paris to attend a seminar at La Jolla. She asks Brandon to meet her at the airport, claiming to have just a four-hour layover. She actually has a week until the beginning of her seminar, but Brandon breaks her heart by revealing that he is dating Kelly. When he sees her back to her hotel room, they share a passionate kiss. Steve and Griffin organize a holiday rave at an abandoned house. Valerie helps them out in the hopes of getting back in Steve's good graces. David and Clare accidentally post the notice about the event on a computer bulletin board for lesbians, who constitute most of the guests. The house has very poor wiring and continually blows fuses. Griffin uses too much electricity, and the house catches on fire. Ray rescues Steve and Valerie, who were fooling around in one of the bedrooms. Kelly and a girl named Allison are trapped in a downstairs bathroom with no means of escape. The firefighters try to reach them as they are engulfed by flames.

On their semester break, Dylan and Brandon take a motorcycle trip through California and they end up being subjected to slave labor by a Native American sheriff for trespassing on a reservation, which helps dissipate the tensions between both of them over Kelly. Meanwhile, Kelly benefits from attending psychology workshop seminars run by a famous, psychology professor named Patrick Finley. Donna tries to help Ray get over his stage fright on the eve of his debut at the grand opening of the Peach Pit After Dark. Steve spends the weekend moping over his father, Rush, taking over the Peach Pit After Dark club from him.

The gang goes to Palm Springs for the national KEG/ALPHA fraternity/sorority convention, where Steve tries to find the perfect woman for himself after he rejects the blind date his father sets him up with. But Steve gets more than he bargained for when he meets a shady women named Elle. Kelly spends a day shopping with Alison in which David and Clare misinterpret their relationship as something else. Jim and Cindy put their house up for sale before moving away to Hong Kong. Meanwhile, Donna brings Ray along to make up with him, but later regrets it when he injures her during a fight, while he manages to stay on the good side of her mother. In another part of town, Dylan and Charlie meet with Tom Rose, a mobster-type businessman as a potential backer for their film who agrees to finance their movie, but only if Tom's beautiful, but untalented mistress, gets the lead role.

In Palm Springs, Brandon reacts coldly to Kelly after mistakenly thinking that she and Allison are more than friends; he considers surrendering to Valerie's advances toward him. Things get even worse for Brandon after he's arrested for driving Valerie's car when he's pulled over by a traffic policeman, who finds Valerie's marijuana stash in it. Meanwhile, Steve finally learns Elle's secret of being "more than a woman." Donna decides to give the possessive Ray a second chance, and rudely blows off Valerie, revealing she's figured out that Valerie seduced Ray. Also, Tom Rose and his thugs threaten Dylan with death when they catch him phoning agent Christine Pettit to make a background check of Mr. Rose, for they know something about Dylan's father's murder. This prompts Dylan to terminate his partnership with Charlie and return to Beverly Hills, determined more than ever to find the mobster who ordered his father's killing.

Brandon returns to Beverly Hills from his summer job in Boston and at Steve's advice, he helps set up a destructive rave party in his parents vacant house. Valerie welcomes Ginger LaMonica, a visiting friend of hers from Buffalo who's as wild and devious as she, and has an eye for Brandon. Meanwhile, Kelly returns to Beverly Hills with a new boyfriend named Colin Robins, a young artist whom she met while modeling in New York City. Donna hosts a party on her parents yacht, while trying to hide her doubts about her future relationship with Ray. Also, Dylan becomes more and more obsessed with avenging his father's death when he visits his family's storage locker and talks with his father's former prison cell mate.

Donna's mother, Felice, confesses a past indiscretion to her about her involvement in the Rose Bowl tryouts of 1969, causing Donna to question her own innocence. Meanwhile, bounty hunter Jay J. Jones returns and asks Valerie for help in a divorce case he has by posing as a prostitute in a sting operation to catch the husband in the act. A revenge-seeking Ray charges Joe with battery over their Halloween encounter, resulting in Joe being suspended from CU's homecoming football game. Also, Steve tries to protect the CU mascot, the Golden Condor Head, from the rival college. Brandon mourns the departure of Dylan from Beverly Hills, and Susan encourages him to write a paper about Dylan's plight.

At a frat party Steve hosts at Casa Walsh, things take a turn for the worse when Steve's two teenage half-brothers, Ryan and Austin, start drinking excessively in which Ryan passes out and almost dies from alcohol poisoning. When Rush finds out, being arrogant and narrow-minded as usual, naturally blames Steve for the near-disaster. Valerie brings Colin to the party, who's between incarcerations. Meanwhile, Tara gets out of rehab and moves in with Kelly, Donna and Clare at the beach front apartment. Also, Kelly invites Greg, a med-student from the rehab center, over to the party and whom ends up saving Ryan's life.

Carl hosts Steve's weekend long 21st birthday bash on the ship Queen Mary in Long Beach, where the music group "The Goo Goo Dolls" entertains. Carl then asks Steve a favor: to have a chance with Clare who he has had a crush on. David and Donna grow more intimate while their producer Erik, makes a move on Donna and other women as well. Andrea Zuckerman arrives in town to have fun at Steve's party, and Nat brings Joan along who keeps feeling unwell. Meanwhile, Valerie hires an FBI agent, named Richard Ballen, to find Colin who's in the area trying to get access on a ship to take him to South America. Also, Susan tells Brandon that she has decided to leave town to accept a job offer at a newspaper company in Washington D.C. which makes him wonder if he has a future with Susan after all.

David and Mark throw a big party at their Hollywood Hills house, until a huge brush fire stops the party which brings back a bad memory for Kelly over the house party fire (back in Season 5) and puts Donna in jeopardy when she attempts to save a baby deer. Steve's flirtation results in serious consequences from Clare, while Brandon and Tracy become closer. Meanwhile, Kenny tells Valerie to keep distant from him while he is proceeding with the divorce from his wife. But when Valerie accidentally finds out that Kenny does not plan on leaving his wife, ever, out of respect for their six-year-old son, she later tells Kenny some unsettling news about her.

The increasingly manic-mannered David takes Valerie, Steve and Clare for a wild weekend to Las Vegas where his increased drinking and gambling threaten to turn the events bad, and Ray Pruit is performing at their hotel. David ends up picking up two prostitutes and takes them to a seedy motel where they drug and rob him. David is forced to call Donna for help who arrives in Vegas to comfort him. She yells at Steve, Clare, and Valerie for letting David get out of control. Meanwhile, Kelly finally asks Mark to spend the night with her. Also, Brandon befriends Melanie, a diminutive young woman passing through town and who gives him advice on his future career.

After Brandon breaks up with Tracy, Valerie's meddling jeopardizes his future with Kelly when Val sends Kelly a phony letter from the departed Dylan to test her true feelings for Brandon. Meanwhile, Donna persuades Felice to accompany her to the KEG/ALPHA spring campus talent show, where she gets increasingly worried when a former boyfriend of Felice's (from 'Things to Do on a Rainy Day') shows up to accompany her. Also, Clare takes the stage to sing her favorite song due to a suggestion from Steve, who thinks the idea's all wet when he hears her awful singing voice during rehearsals.

On the day before commencement, Kelly becomes determined to oust Valerie from the Walsh house (and town) and pressures Brandon to do so. Meanwhile, Donna decides it's time to move up to a new level of romance with David after getting advice from her grandmother. Steve plans to pull the "best senior prank ever" with some help from his frat brother Muntz, as well as David.

On the day of graduation, a broke and lonely Valerie disrupts Kelly's plans when she takes off on a mindless spree causing Brandon to delay the ceremony to look for her. Kelly's father, Bill, throws a 1920s nostalgic post-graduation party for the class and has the The Cardigans band perform. He also tries to make up with Kelly, who continues to push him away. Steve's stepbrothers, Ryan and Austin, show up for festivities where Ryan is drawn to Kelly's half-sister, Joy. Also, Steve's plans for Clare derail due to her decision to move to Paris with Chancellor Arnold, which leads to Steve and Clare breaking up for good.

When a sex shop opens, Steve & Brandon want to cover it for the Beverly Beat. Kelly is not happy with the idea. When they also invite David and Muntz to join them, David gets a little crazy and buys stuff that Valarie doesn't like.

With a few hours before Brandon and Kelly's wedding, they continue to feel uncertain about the path they are on. Jim and Cindy Walsh arrive in town from Hong Kong to help plan Brandon and Kelly's wedding. Meanwhile, Valerie finally decides to get an AIDS test after Johnny confesses to her that he happens to be HIV-positive, and she asks David to come along with her for emotional support. Steve becomes dateless for the wedding when Sarah decides to go back to her husband after witnessing her friend's messy break up. After the caterer, Jacob, saves Donna's life, Donna agrees to go on a pretend date with him to make his ex-girlfriend jealous. This makes Noah jealous.

Dylan whisks Kelly away on a plane to Mexico to be with her, while he uses the trip to smuggle heroin into the USA for his own use. Gina continues to woo Dylan to know him, while Matt becomes jealous over Dylan's constant presence around Kelly. Meanwhile, the Brian Setzer Orchestra is featured at an AIDS-benefit dance marathon at the After Dark where Steve overextends himself when he inadvertently pledges $12,000 to sponsor a couple who turns out to be his former fraternity brother, Muntz, and his wife. Also, Sonia's girl gang member friends affect Donna's business at the boutique shop "Now Wear This!" by their presence. When the store is robbed one night, the missing Sonia becomes the chief suspect. Noah also asks Gina to help him and Nat plan Donna's 24th birthday party for Christmas Day, where Gina has a little too much to drink and finally reveals her true contempt feelings about Donna in front of everyone.

David and Donna announce their engagement in which all of their friends rush to give them the perfect wedding with Donna's mother, Felice, and Kelly's mother, Jackie, taking over the arrangements and Nat catering for the ceremony and agreeing to escort Donna down the church aisle. Meanwhile, Steve asks Janet to help him form their own publishing company so they both can have time for baby Maddie. Noah returns to Ellen and tells her that he has decided to give their relationship a second chance. At Donna's pre-wedding party, Kelly, Janet, Felice and Jackie are in attendance as well as friends from their past who include West Beverly High principal Mrs. Yvonne Teasley, as well as Andrea Zuckerman and even Valerie Malone. At David's bachelor party, Steve, Noah, Dylan, Nat, and David's father Mel attend the gathering as well as Steve's stepbrother Ryan and former KEG fraternity brother Munz, except for Brandon Walsh who sends his regards to everyone via videotape. The day of the wedding goes without a hitch and at the end, Matt shows up briefly to tell Kelly that he has decided to move back to New York, and she goes back to try to renew her relationship with Dylan.