Rory returns to Stars Hollow after spending the summer interning in D.C. Her homecoming is bittersweet as she finds herself faced with a decision between Dean and Jess. Lorelai ponders her future when she discovers that Christopher's girlfriend is pregnant.
Emily tries to bring Christopher back into the family which leads to an angry confrontation between him, Lorelai and Rory. Lorelai tries to avoid a romantic pursuit from a dorky suitor.
Rory's application to Harvard arrives and she panics when she realizes she's just like every other neurotic senior girl with a long list of activities and a 4.0 GPA. Meanwhile, Lane advertises for rock musicians and falls for one of the prospective rockers.
Lorelai is invited to speak to Rory’s old school about her career, but when the questions turn instead to her pregnancy, several of the parents freak out. Rory is jealous of Jess’s new trampy girlfriend and Lane decides to dye her hair purple to shock her mother.
Lorelai meets an attractive man at an auction organized by her mother. But when the first date is a disaster and she tries to cancel the second date, Emily accuses her of damaging her social reputation. Meanwhile, Rory enlists Jess' help when a neighbor's sprinkler goes haywire.
Lorelai drives Rory to Boston, intending to drop her off at Sherry's baby shower, but when she gets there, Sherry corners her into staying. Meanwhile, Luke grows suspicious about Jess's finances when he buys a car.
Lorelai makes Rory her dance partner in an effort to win an annual dance marathon.
Richard gets Rory an interview with Yale University's dean of admissions.
Lorelai and Rory circulate among various friends and family on Thanksgiving Day.
Rory and Jess bump into Dean while at Star Hollow's winter carnival. Great-Grandmother Gilmore makes a surprise visit.
Francie manages to convince Paris that Rory is plotting against her. Lorelai and Sookie meet two attractive men while at a seminar.
Lorelai's beau, Alex, invites her to go fishing. Paris attempts to have Rory impeached by the student council. Lane works on a plan to get Dave as her prom date.
When Sherry goes into labor with only Lorelai and Rory present, Lorelai reflects on her own experiences with her pregnancy and the birth of Rory.
Lorelai and her new boyfriend go to New York for the weekend. Jess is sporting a mysterious black eye.
Rory gets fed up waiting for Jess and goes to a hockey game with Lane. Rory runs into Dean and his new girlfriend, Lindsay. Lorelai confronts Jess about his poor treatment of Rory. Gran comes to stay with the Gilmores for a few days and Emily catches her kissing a man.
Rory waits for college acceptance letters and ends up competing with Paris for the honor of giving a speech at Chilton's Bicentennial. Lorelai runs into her ex-fiance Max and, after the two share a kiss, begins to wonder whether she made a good decision in terminating their engagement.
A fire at the Independence Inn during a meeting of the Edgar Allen Poe Society leaves Lorelai scrambling to find a place to stay for the inn guests, which turns out to be her house. Luke confronts Jess about missing school to work at Walmart full-time, while Rory tries to coax Paris out of her bedroom seclusion.
While Lorelai is helping with the rebuilding of the inn, Richard comes to offer her money off of an investment made when she was a baby. To Emily's dismay, however, she uses part of it to repay her parents for Rory's education costs. Meanwhile, Rory plans to hold a birthday pizza party for her mother, and Luke confirms his suspicions about Jess' skipping school to work at Wal-Mart.
Jess and Dean's longstanding dislike for one another comes to blows during a bash where Lane's band is set to debut.
Rory and Jess have difficulty dealing with one another following his fight with Dean at the party. Lorelai and Sookie find themselves with an opportunity to buy their dream inn. Jess' long-lost father, Jimmy, shows up to reach out to Jess, but inexplicably vanishes once again. Meanwhile, Luke discovers that Jess has flunked out of high school and warns him to either repeat the final year or leave.
Following his heated argument with Luke, Jess exits Stars Hollow and goes to stay with his father, Jimmy, in Venice, California, who doesn't know how to raise a son, but allows him to stay. Meanwhile, Lorelai wonders how to tell Rory about Jess' departure and learns that because of the money Richard gave to Rory, Rory is ineligible for financial aid from Yale.
Lorelai and Rory continue to plan their trip backpacking across Europe as Rory's graduation approaches, despite the matter of the Independence Inn's potential sale. After learning that Lorelai has made a huge sacrifice in order for her to attend Yale, Rory springs into action, determined to rectify the situation. Emily and Richard agree to help out, and, after a moving valedictorian speech, also present Rory with a car.