Newly retired Richard is driving Emily crazy, so Lorelai is coerced into taking her father for a day in Stars Hollow, where he proceeds to drive both Lorelai and Rory batty while criticizing every aspect of their lives and refusing to let Rory accept the car that Dean has built for her.
During the annual Stars Hollow charity picnic basket auction, both Lorelai and Rory's baskets have more competition then they both anticipated. Meanwhile Jackson refuses to bid on Sookie's basket leading them to work on their communication. Rory and Lorelai have their own communication problems but work it out after Emily sides with Lorelai's initial reaction to Jess worming his way into Rory's life.
Christopher and his girlfriend Sherry visit Stars Hollow leading Sherry to push for a Friday night out alone with Rory to bond. So Lorelai takes Christopher to a tumultuous Friday night dinner at her parents. Lorelai, thinking she missed out on a life with Christopher, confesses her self-realization.
Rory panics when she suddenly realizes that she lost the bracelet Dean made for her, and when a suspicious Lorelai catches Jess in Rory's room, she accuses him of stealing the bracelet. Meanwhile, Luke goes a little stir-crazy after living with Jess in the tiny apartment over the diner, and he impulsively buys the building so he can expand.
Lorelai and Emily spend a weekend at a health spa, but they sneak out for some real food at a local restaurant where Emily dances with a distinguished stranger, then blames Lorelai for her feelings of guilt. Back at home, Rory looks forward to a rare evening alone, but when Paris, Jess and Dean all drop by to keep her company, the sparks fly.
Lorelai and Rory help out at the diner while Luke is left to plan his unpleasant uncle's funeral, which causes him to reflect on his own existence. Meanwhile, Emily lends a hand planning Sookies wedding and the skies the limit.
After helping Rory out with her business project for the annual Chilton Business Fair, Richard realizes retirement isn't for him. Meanwhile Dean, for good reason, is feeling insecure about Rory. Michel's mother visits and their once great relationship is over after Lorelai interferes.
Luke asks Rory to tutor Jess who is close to failing, but Jess uses it to get closer to Rory and when they get into a car accident, Lorelai takes it out on Luke for taking Jess in to begin with. Lorelai takes over the movie selection for the town square movie night, but in the end realizes why Taylor chooses the same movie every year and Kirk uses the night to show of his work.
Lorelai helps her dad open his new office and gets the cold shoulder when she tells him she has a job already. Rory tries to let everyone know Jess wasn't the only one at fault for the accident and with a new music store in town, Lane discovers her new love.
After doing her best to avoid Luke, Lorelai can't avoid the inevitable, but Luke isn't ready to patch things up yet. Rory invites her grandparents to her mom's graduation, but misses it herself after cutting school to meet Jess in New York.
It's Sookie's wedding day and Jackson is wearing a kilt. Jess and Rory happen to see each other before the wedding, which Rory and Lorelai are part of. Chris has to leave because his girlfriend calls with some news.
Rory returns from Washington just in time for the First Annual Stars Hollow End of Summer Madness Festival where she realizes her feelings for Jess might be a lot stronger then she thought, but is it too late to do anything about it? Lorelai is having strong feelings of her own.
Christopher tries to talk to the Gilmore girls, but Emily saves the day. Francie tries to assert her power on the student council. Meanwhile Rory and Jess have it out about their hurt feelings and are Lorelai and Kirk dating?
As college nears, Rory receives her Harvard application leading her and Lorelai to have lunch with an alumni to see if she stands a chance at getting in, but the college talk has Dean worried about their future. Meanwhile Taylor decides to open an old soda shop next to Lukes and Lane advertises for a band member.
Lorelai is cornered by a new local and talked in to watering his garden whilst he's away on a business trip. When Lorelai has to get to work, she asks Rory to take over, but when things go wrong she has to enlist Jess' help. Lorelai also asks Emily for help finding a guy she met at an auction house, but realizes he's not quite what she anticipated.
Rory is invited to Sherry's baby shower and Lorelai gets pulled in with her. Between Sherrys good will and the party poppers, Lorelai is at her breaking point and feels the need to let off some steam. Jess comes home with a car and the town gathers for a not so successful town demonstration.... stop the noodle shoes????
Sore from the dance marathon and the break up with Dean, Rory and Lorelai adjust to having Jess and Rory going together. Richard corners Rory and invites her to a Yale reunion where he has more plans then he tells her. Rory apologizes to Dean and Lorelai and Rory both consider Yale.
Rory and Lorelai work to fit in four thanksgiving dinners but they don't eat much at the family dinner when Lorelai finds out Rory applied at more colleges then just Harvard. Lane has her first kiss and human Kirk and cat Kirk have a little adjusting to do.