After Richard and Emily invite Rory and Lorelai to their fancy tailgate party at the Harvard/Yale football game, Lorelai’s innocent conversation with Richard’s ex-fiancée, Pennilyn Lott, leads Emily to realize that Richard and Pennilyn have been meeting secretly for lunch for many years. Emily berates both Richard and Lorelai, prompting Lorelai to stop worrying about her mother’s feelings and finally accept Jason’s invitation to dinner instead of staying at Emily’s party. Meanwhile, Richard introduces Paris to his former classmate Asher Flemming, who is now a distinguished Yale professor. Later, Rory is astonished when she later spots Paris and the professor kissing.
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Lorelai is disappointed when Rory insists on keeping her promise to Lorelai's parents, and eats dinner at their house on her and Lorelai's last night together before school. When Emily and Richard keep Rory hostage for the entire evening, Lorelai overcomes her distaste for visiting her parents in order to be with Rory.
Mother and daughter share Rory's first day at Yale University by moving Rory into her dormitory, where she meets a strange new roommate, Tanna, and learns that her old adversary, Paris, will also be sharing her room. Although she is overwhelmed with excitement, Rory is also embarrassed to find that she isn't quite ready to let Lorelai go. Meanwhile, Luke continues to cope with the aftermath of a disastrous cruise with his soon-to-be-former wife.
Rory is shocked when Emily completely redecorates Rory's dormitory room without her permission. At her first Yale party, Rory finds herself trapped by twins who were instructed by Emily to find Rory and keep her safe. Meanwhile, Lorelai and Sookie take a job catering a kids' "Lord of the Rings"-themed birthday party to make money while their new inn is under construction. And Richard takes on a new business partner named Jason "Digger" Stiles, who is the son of Richard's former associate.
While visiting Stars Hollow for the weekend, Rory encounters her ex-boyfriend Dean, who awkwardly invites her to his wedding the next day. During his bachelor party that night, Dean stumbles into Luke's diner and drunkenly confesses how much he misses Rory. Meanwhile, Taylor Doose, who controls the permit procedures for every building in town, irritates Lorelai and Sookie as they try to get construction started on their new Dragonfly Inn.
Rory goes on her first date since ending her relationship with Jess and finds that college dating is not going to be easy. Lorelai invites Luke over for the traditional movie night she used to share with Rory. Later, Lorelai gets upset when she learns that the designer she just hired for the Dragonfly Inn used to work for Emily.
When Emily plans an elaborate launch party for Richard's new company, she hires Lorelai and Sookie to cater the affair but insists they prove that they are worthy of her trust. After Richard's partner, Jason "Digger" Stiles, insults Emily by suggesting that her party idea is outdated, Lorelai confronts him and is surprised when he asks her out to dinner. Meanwhile, Rory has a tough time finding a decent place to study at Yale.
Stars Hollow hosts the Festival of Living Art, an event in which the townspeople dress up and present tableaux imitating famous paintings. Rory appears in Portrait of a Young Girl Named Antea. Lorelai plays the beauty in Renoir's The Dance at Bougival. And Kirk is Jesus in The Last Supper, along with the Town Troubadour as Judas. Meanwhile, Sookie panics because she hasn't given birth by the date she's supposed to, and Lorelai calms her with stories of the night Rory was born. Luke's wife, Nicole, tells Luke that she wants to postpone their divorce and give their relationship a chance. And Lane finds a great guitarist, Gil, but he is a lot older than everyone else in the band.
When the editor of the Yale student newspaper tells Rory that her articles are dull, she writes a scathing review of the Yale ballet and becomes the vindictive lead ballerina's target. Jason impresses Lorelai by manipulating Emily into inviting him to Friday night dinner so he can continue flirting with Lorelai. Meanwhile, surprised to see Nicole at the diner, Lorelai forces Luke to admit that he and Nicole have put their divorce on hold and are dating again. And Lane gets upset when her mother gives her a "marriage jug" to send to her boyfriend in California.
After Richard and Emily invite Rory and Lorelai to their fancy tailgate party at the Harvard/Yale football game, Lorelai's innocent conversation with Richard's ex-fiancée, Pennilyn Lott, leads Emily to realize that Richard and Pennilyn have been meeting secretly for lunch for many years. Emily berates both Richard and Lorelai, prompting Lorelai to stop worrying about her mother's feelings and finally accept Jason's invitation to dinner instead of staying at Emily's party. Meanwhile, Richard introduces Paris to his former classmate Asher Flemming, who is now a distinguished Yale professor. Later, Rory is astonished when she later spots Paris and the professor kissing.
While Lorelai and Sookie work on renovating their new inn, Michel clashes with a rival who he believes wants the manager position promised to Michel. Meanwhile, Lorelai happily spends a romantic night at Jason's house, despite his many eccentricities. But she is concerned to learn from her parents, who don't know that she and Jason are dating, that Jason was seen escorting another woman to a charity function. Rory remains irritated by Paris' disturbing relationship with her much older professor, Asher Flemming. And the incredibly efficient Lane intimidates Luke when she begins waiting tables at his diner.
Lorelai is upset to find out that Luke has gotten an apartment with Nicole in another town in Connecticut. However, when Lorelai realizes he is reluctant to move, she admits to him that she doesn't want him to leave Stars Hollow. Meanwhile, Rory remains attracted to a fellow student, William, after he rebuffs her invitation to date, and she is later humiliated to learn that he has been gossiping about her obsession with him. Also, when Lane sneaks out to perform with her band, Mrs. Kim finally discovers her daughter's secret life and tells her to move out of the house.
Luke is wary when his flighty sister Liz arrives for an unexpected visit. Lorelai promises Jason that she will tell her parents about their relationship, but she reconsiders after Emily comments about how laughable it would be if Lorelai and Jason began dating. Meanwhile, when Paris confesses to Rory that her affair with the professor is becoming serious, Rory reminds Paris how badly she is treating her boyfriend, Jamie --so Paris breaks up with Jamie. Finally, Luke discovers that Jess' car is missing and reports it stolen, but he later discovers that Jess has come back to town to pick up the car. Rory sees Jess sleeping in his car but walks away without speaking to him.
Stranded in Stars Hollow while his car is being repaired, Jess keeps crossing paths with Rory--but he walks away from her every time. Luke tries to talk to Jess about Liz, Luke's sister and Jess' mother, who is dating someone new. However, Jess angrily tells Luke to stop interfering in other people's lives. Lorelai does a favor for Emily by attending a charity dinner and is pleasantly surprised when her secret boyfriend, Jason, arrives--and the unsuspecting Emily asks them to "pretend" they are a couple. Meanwhile, when Rory and Jess encounter each other for a third time, Rory tries to be the one who walks away, but Jess stops her and makes a shocking confession.
Although she is completely exhausted by her heavy workload at Yale, Rory is horrified when a professor suggests that she drop a class. She confesses her self-doubt to her former boyfriend Dean, who is working on the construction crew at the Dragonfly Inn. Meanwhile, frustrated because she can never reach Rory and by the nonstop work involved in getting the Dragonfly ready to open, Lorelai first accuses Sookie of not doing her fair share then turns to Luke for help and advice. Also, Richard becomes infuriated when he and Lorelai both get a sample of the nastiness that Gran usually reserves for Emily.
Rory encounters Dean for the second time at the Dragonfly Inn and gets a glimpse of his new life. Later, Lorelai and Rory decide to spend a day together at the mall, but they run into Emily and are caught up in her wild shopping spree. When Lorelai questions her mother on her out-of-control spending, Emily admits that she is getting revenge on Richard, who has been ignoring her to concentrate on his new business. Meanwhile, although Lane is excited to be moving into her first apartment with two of her band mates, she is also hurt by her mother's coldness.
When Gran dies suddenly, Richard has an emotional breakdown. Emily handles the funeral arrangements with her usual efficiency--until she finds a letter Gran had written to Richard years earlier, begging him not to marry Emily. Lorelai is forced to take over the preparations, leading to her own small breakdown while buying new clothing for Gran to be buried in.
Exasperated by the freezing Connecticut weather, Rory and Paris travel to Florida for their first spring break. Amidst sun, sand and too much partying, they meet Madeline and Louise, their pals from Chilton. Rory is shocked when Paris makes an unexpected bid for attention at a nightclub where musical group THE SHINS (themselves) are performing. Meanwhile, Lorelai's relationship with Jason takes another step forward when he gives her a key to his home. And Luke needs Lorelai to bail him out of jail after he reacts badly to the news that his estranged wife is dating another man.
Jason's father, Floyd, sues Jason and Richard for taking his clients. Floyd also reveals that Jason and Lorelai have been dating secretly for months. Meanwhile, Dean upsets Rory when he admits he has dropped out of college to work full time so he and his wife, Lindsay, can buy a townhouse. Lindsay demands that Dean stop associating with Rory, but Dean and Rory plan to secretly remain in contact.
When Jason reveals that he is no longer in business with Richard, Lorelai has an ugly confrontation with her father about his treatment of Jason. Later, after an extremely uncomfortable Friday night family dinner, Lorelai and Rory spy on Emily and make a shocking discovery about the state of the elder Gilmores' marriage. Meanwhile, Luke tells Lorelai that he and Nicole are getting a divorce.
Depressed over the failure of his marriage, Luke resorts to a self-help tape and suddenly realizes that he already knows who his soul mate is. Later, when his sister Liz returns to town and announces that she and T.J. are getting married, Luke finds Jess and convinces him to attend the wedding. Meanwhile, Lorelai is completely stressed as opening day at The Dragonfly Inn approaches, and Rory pretends not to be interested when Lorelai tells her she overheard Dean and his wife, Lindsay fighting.
All the townspeople of Stars Hollow come to Liz's Renaissance-themed wedding. Jess walks Liz down the aisle, and Lorelai and Luke share a romantic dance, after which Luke asks Lorelai out on a date. Meanwhile, as Yale students begin their summer break, Rory attends a drunken party and has to call Dean to drive her back to the dorm. Dean tries to explain his unhappy marriage to Rory, but they are interrupted when Jess arrives and makes Rory a surprising offer.
Lorelai suspects that Luke's intentions towards her have become serious, but she doesn't have time to dwell on the situation as she prepares for the opening of the Dragonfly Inn by inviting friends and family to a test run. Using the opportunity to force her parents to reconcile, Lorelai is shocked when it becomes obvious that the damage to their marriage is greater than she had thought. When Jason arrives at the Inn to convince Lorelai that their own breakup was a mistake, Luke tries to declare his true feelings for Lorelai. Meanwhile, after their last awkward encounter, Rory attempts to salvage her friendship with Dean.