Lorelai tells Luke about Max and his proposal, and accepts it. Also, Lane's parents got her a one-way ticket to Korea for the summer, which frightens her. Rory invites Dean over for Friday night dinner, because they are celebrating her getting into the top 3% in her class. Tension rises between Dean and Richard when he accuses Dean of not being good enough for Rory, causing her to fight with her grandfather and causing Emily to fear that they'll lose Rory.
Rory begins to stress because she is falling behind on extra curricular activities, leaving her with less time for Dean. Also, Rory and Richard make up, while Emily and Lorelai get into a fight because Lorelai did not tell her about Max and his proposal.
Rory, Sookie, Michel and Emily go to a club for Lorelai's bachlorette party, where Emily tells story about her and Richard's wedding. Lorelai notices how everyone else's relationship is different than hers, and begins to have doubts about the wedding. When Rory and Lorelai get home, Lorelai says that she is calling the wedding off, and that they are going on a road trip.
Rory and Lorelai take a road trip to Harvard, where Rory fits right in. She feels like this is the place for her. When they return home, Lorelai cries when she sees the chuppah that Luke made for her, while Luke comforts her. Seeing how Rory is growing up, Lorelai decides to start planning for her own inn.
Luke's sister Liz feels like her son Jess is getting into too much trouble and asks Luke to take care of him. Lorelai decides to throw Jess a welcome party, but at the party Jess is only nice to Rory. Luke receives phone calls about Jess stealing money and lawn gnomes and tries to talk to Jess, but becomes too angry, and pushes him into the lake. Later, Luke goes to confront Jess and lays down his new rules. Meanwhile, Paris is trying to make Rory's life miserable at 'The Franklin' by assigning to interview Mr. Medina.
The annual debutant ball is coming up, and Emily's friends are nagging her to put Rory in it. When Emily asks Rory, she accepts, to Lorelai's dismay. Emily hopes that the ball will help bring Richard back into their social circle, but instead, it makes him angry, and causes them to fight at the ball. Also, Christopher agrees to present Rory and shocks Lorelai with news about his new relationship.
The Headmaster Charlton tells the Gilmore girls that they need to improve on their social skills. Rory tries to socialize by sitting with some girls at lunch, but sits with the'Puffs', a secret society at Chilton. The Puffs accept Paris and Rory into their group and have a ceremony to welcome the new members by kidnapping them and breaking into the Headmaster's office at school. Unfortunately, they get caught by Headmaster Charlton. Meanwhile, Lorelai joins the Booster Club, and offers the inn to them for their fashion show.
Lorelai and Sookie start up their plans to open an inn, but get stalled when the owner of the inn refuses to sell the property. The unexpected arrival of Mia, the owner of the Independence Inn, makes Lorelai feel guilty about wanting to leave the Independence Inn. However, Mia is supportive of their plans and tells everyone that she's planning on selling the inn. Emily confronts Mia in order to meet the woman who was such an important part of both Rory and Lorelai's life. Meanwhile, someone planted a fake hug scene in front of Doose's market. Rory tells Jess that she knows he's the culprit, how he's a jerk for letting Luke take all the heat from everyone in Stars Hollow. He agrees to lighten up and be more considerate of Luke.
Lorelai goes on a 'casual date' with Paul, one of the students in her business class. When Paul comes to the diner, Luke and the rest of the town make fun of Lorelai for dating someone so young. Sookie tells Lorelai that Luke has a crush on her and seeing her dating other guys makes him jealous. Meanwhile, Rory has to perform the final scene of Romeo and Juliet with Tristan, making Dean angry. At the performance, Tristan is pulled from school after a prank and Lorelai lets Luke know that that he'll always be a very important part of her life.
A snowstorm prevents the Bracebridge group from having a historical dinner at the Inn so Lorelai and Sookie invite their friends to the dinner. At dinner, Richard confesses that he quit his job and Jess tries to work his way between Dean and Rory.
When Lorelai's house gets termites, Rory defies her mother and tells Emily about Lorelai not being about to get a loan. After not being able to come up with another way, Lorelai is forced to ask Emily to co-sign a loan with her. Meanwhile, Lane decides to become a cheerleader, straining her friendship with Rory.
Emily sends Richard to spend the day with Lorelai in Stars Hollow. Richard passes judgment on every aspect of Lorelai's day, from what she eats for breakfast to how she runs her business. Meanwhile, Rory inadvertently gets the video store to censor its movies and Dean comes over with a surprise for Rory.
At the Stars Hollow picnic basket auction, Jess outbids Dean for Rory's basket, winning the chance to have lunch with Rory and causing Rory and Dean to fight. Jackson doesn't bid on Sookie's basket after thinking she doesn't want to move in with him, but they reconcile when he buys back the basket, then proposes to Sookie. Miss Patty attempts to set Lorelai up but Luke comes to the rescue and bids on Lorelai's basket. After listening to Dean's concerns about Rory and Jess, Lorelai and Rory fight over Dean confiding in Lorelai.
Christopher returns to town and brings his girlfriend, Sherry, along. Sherry wants to bond with Rory since her and Christopher are becoming serious. Emily finds out about Sherry and tells Lorelai that she has always wanted her and Christopher to end up together. Lorelai tells Christopher that she's always thought that they would get back together, too, and that's why she's never had a relationship that lasted. Christopher gets angry for Lorelai blaming him for her bad relationships, leaving Lorelai hurt while Luke watches.
Luke decides to find a new, bigger place to live, and with Lorelai's help, he finds one that he likes. But after finding out that Taylor owns the apartment, Luke throws out his application and buys the building next to his diner. Meanwhile, Dean notices that Rory isn't wearing the bracelet he made her, sending Rory into a panic to find the bracelet.
Emily and Lorelai go to a spa together for the weekend and Emily tries to bond with Lorelai by booking them to do everything together. At home, Rory plans on having a quiet night alone but Paris, Jess and Dean all come over, resulting in Paris taking the blame for Jess being there and realizing Jess's feelings.
Lorelai and Rory help Luke at the diner while he plans his uncle Louie's funeral. However, none of Louie's friends attend the funeral but they all come together for a reception for Louie at Luke's. Meanwhile, Emily helps Sookie plan her wedding and Rory forces Jess to help Luke out more.
Richard helps Rory's group create a product for the Business Fair at Chilton. Richard becomes too involved in the project and takes it personally when the group doesn't win first place. Later, Richard decides to start a new business and Dean tries to be close to Rory after fearing that he's losing her to Jess.
Luke asks Rory to tutor Jess, which goes okay until they decide to go for ice cream and get into a car wreck with Jess behind the wheel. Rory gets sent to the hospital with a broken arm and Lorelai blames Luke for the accident. Christopher arrives to take care of Rory and Luke sends Jess home.
After the accident Rory is mad to find that everyone blames Jess for the accident. Luke closes the diner to go fishing. Meanwhile, Richard opens a new office and Lorelai helps him after his old secretary declines transferring to Richard's office and Lane finds that her dream in life is to be a drummer in a band.
Rory invites Emily and Richard to Lorelai's graduation from business school but misses the graduation when she gets a call from Jess and cuts school to visit him in New York. Lorelai forgives Rory after she sees that Rory has fallen for Jess.
Christopher returns to town for Rory's cast removal and decides to stay for Sookie's wedding. Christopher tells Lorelai that his relationship with Sherry is over and they rekindle their past romance. However, Sherry calls with startling news and Christopher returns to Boston, devastating Lorelai. Meanwhile, Paris gets Rory to run as her vice-president in the student body elections and win, which means Rory will have to spend the summer in Washington D.C. Jess returns to Stars Hollow and asks Luke if he can stay. At the wedding, Rory sees Jess and they kiss, but Rory runs off as the wedding begins.