Lorelai and Rory return from their trip to Europe to a waiting, busy life, including the impending birth by the very pregnant Sookie. After misreading the Yale orientation start date, Rory realizes she only has two days as opposed to a week to get ready, leading to a frantic packing marathon.
Lorelai helps Rory move into her new dorm at Yale, but Rory realizes that separating from her mother won't be so easy. She encounters her strange roommate, Tanna, and to her dismay, learns that Paris will also be sharing the room with them. Meanwhile, Luke is still troubled by the cruise fiasco with Nicole.
Rory gets a surprise when she discovers that her dorm room has been redecorated by Emily without her approval. She is also smothered with attention when Emily tries to watch her back by sending escorts for her at her first college party.
Rory comes back to Stars Hollow for the weekend and runs into Dean, who invites her to be a guest at his wedding the following day. Dean later confesses to Luke in a drunken stupor that he may have been foolish to let Rory get away. Meanwhile, Lorelai and Sookie butt heads with Taylor over their building permit for the Dragonfly Inn.
Rory goes out on a date, her first since the breakup with Jess, while back in the dorm, her roommates stubbornly try one another's patience. Lorelai stews over the fact that the Dragonfly Inn's designer once worked for her mother when she invites Luke to fill in for Rory on their usual movie-watching night.
Emily hires Lorelai and Sookie to cater a launch party she's designing for Richard's new company, but the would-be caterers find that Emily needs a lot of convincing as to their abilities. The celebration moves elsewhere, however, when Richard's partner, Jason, manages to convince him that Emily's idea of a party is antiquated. Meanwhile, Rory finds it increasingly difficult to find herself a quiet place to study at school.
Stars Hollow puts on a "Festival of Living Art" in which Lorelai, Rory, and Kirk appear in costume as figures within reenactments of classic paintings.
Rory is told that her articles for the Yale newspaper lack pizazz, so she writes a blistering review about the Yale ballet and soon finds herself the enemy of the vengeful lead ballerina.
Richard invites Lorelai and Rory to a tailgate party for a Harvard/Yale football game, but after meeting Richard's former fiancee, Pennilyn, Lorelai learns that Emily suspects Pennilyn and Richard have been meeting up for years.
In the midst of her secret new romance with Jason, Lorelai finds out from her parents that he was spotted with someone else at their charity bash. Rory and Paris are given a rigorous initiation at the Yale newspaper, but when Paris ducks out to rendezvous with Professor Flemming, Rory is left explaining where she went. Meanwhile, Michel ends up babysitting for Sookie, while Lane becomes Luke's new employee.
Lorelai tries to get Luke to stay in Stars Hollow when he shows hesitation in moving to an apartment outside of town with Nicole. Rory is mortified when William, whom she'd been unsuccessfully pursuing, starts telling people she's a little too attached to him. Meanwhile, Lane gets thrown out the hose by her mother when she finds out about Lane's secret rock band practices.
Despite Jason's insistence, Lorelai balks at telling Emily about her relationship with him when Emily dismisses the possibility that such mismatched people could ever being a couple. Paris breaks up with her boyfriend at Rory's urging in order to continue seeing the professor. Meanwhile, Luke has his hands full with both a visit from his unpredictable sister and the return of Jess.
Jess hangs around Stars Hollow while he waits for his car to be fixed and, to his dismay, keeps bumping into Rory, at which point he repeatedly walks away, but when she tires of his disappearing act, he must reveal a bombshell to her.
Rory finds herself swamped with too many courses, but balks at a professor's suggestion that she drop one of them to help herself out. Lorelai's inability to get ahold of Rory exasperates her during a tumultuous construction period for the Dragonfly Inn, but Sookie ends up as the recipient of Lorelai's venting.
Rory sees Dean again while he works at the Dragonfly Inn and begins to learn about what kind of life he's created for himself in their time apart. Her afternoon with Lorelai doing some mall window-shopping becomes a whole different story when they bump into Emily and tag along on her massive shopping excursion, which Emily hopes will put the sting on an inattentive Richard.
Richard's mother and great Gilmore matriarch, Gran, dies unexpectedly, and Richard falls to pieces, leaving Emily to handle the arrangements. Lorelai soon takes over those duties, however, when Emily discovers that her mother-in-law once secretly warned her son to break off the engagement, but while she soon finds the emotions flooding in, Rory worries that her own reactions about Gran are too su
Rory and Paris head down to warm Florida for their spring break, where they inadvertently see Louise and and Madeline from their high school days, and Paris lets loose while at a nightclub with Rory. Meanwhile, Luke turns to Lorelai for help after a jealous rage over Nicole's new beau lands him in jail, and Jason and Lorelai take their relationship to the next level when he gives her a spare key to his home.
Jason and Richard are sued by Jason's father Floyd for nabbing some of Floyd's clients, at which time Floyd outs Jason's quiet relationship with Lorelai. Meanwhile, Rory learns that Dean is a full-time employee and no longer in college, with plans for he and his bride Lindsay to buy a house using the money. Dean also tells Rory that according to Lindsay, Rory is no longer welcome in his life.
Lorelai confronts Richard and accuses him of mistreating Jason when Jason informs her that he and Richard are no longer business partners. Furthermore, after a subsequently awkward dinner between Lorelai, her parents, and Rory, the younger Gilmore Girls inadvertently learn about the poor state of Richard and Emily's marriage. Lorelai is also informed by Luke about his now-definite divorce from Nicole.
Luke turns to self-help methods after mulling the end of his marriage and begins to realize the identity of his true soul mate. When his sister, Liz, comes back to town to get married, he tries to coax Jess into going to her wedding.
Liz's renaissance-style wedding has the whole town celebrating, including a proud Jess, during which time Luke surprises Lorelai by asking her first to dance, then to go out on a date with him. Meanwhile, when Rory is stranded at a wild off-campus party, she ends up calling Dean for a ride to her dorm, but their heartfelt conversation is cut short when Jess shows up.
Lorelai preps the Dragonfly Inn for its grand opening, using friends and relatives as the subjects of a trial run, but is somewhat occupied by the thought that Luke's feelings for her have grown stronger.