Rory’s father, Christopher, returns, causing tension in Emily and Richard’s house–and forcing Lorelai to make a big decision about her family’s future.
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When Rory gets accepted to a fancy prep school, Lorelai is forced to humble herself and ask her mother for help in paying the tuition.
A t-shirt, shorts and cowboy boots clad Lorelai accompanies Rory on her first day at school, drawing disapproving stares from the other mothers and from Lorelai's own mother, Emily. Lorelai and Emily argue over money for Rory.
When Richard and Rory form an instant bond during a wonderful day of golf, Lorelai feels left out and finds it difficult to observe Rory's emotional connection with Emily and Richard, knowing that she herself lacks the same intimacy.
Rory has trouble getting good grades at her new school. Lorelai becomes interested in Rory's handsome teacher.
Lorelai forgets to tell Rory that she has a date with Rory's teacher Max. Rory has a new crush.
Rory gets upset at Emily, who plans a formal birthday party for her but feels that Rory is being ungrateful when Rory reveals that she would not like to have a formal birthday party. However, Lorelai's party for Rory is a success.
Rory decides not to tell her mother that she and Dean have kissed. Lorelai takes the liberty of inviting Dean over, and Rory is embarrassed by her mother's actions.
Lorelai shares a wonderful day with Max while Rory is snowed in at her grandparents home. Lane misses Rory and comes to visit.
Rory turns down two boys' offers to take her to a school dance and instead chooses to go with Dean. Dean gets into conflict with the two jealous boys, who were rejected by Rory. Dean and Rory fall asleep together inside of Miss Patty's dance studio. When they wake up, Rory rushes home, only to hear her mother and grandmother in a passionate argument about Rory ending up like her mother.
Richard collapses at the Gilmores' Christmas party. Dean assures Lorelai that nothing improper happened on the night he and Rory fell asleep together. Lorelai and Luke seem to be more attracted to each other.
Paris exposes the relationship between Lorelai and Rory's teacher, Max, causing a scandal. Lorelai and Max sadly part. Rory furiously confronts Paris, who admits that she wanted to deflect attention away from her parents' embarrassing, high-profile divorce. Sympathetic, Rory befriends Paris.
Lorelai finds herself on a hellish double date with Sookie, Jackson and Jackson's very odd cousin. Meanwhile Rory double dates with Dean, Lane and Dean's friend. They keep their plans secret because Lane's protective mother would not approve.
Trouble occurs when Rory brings her friends to a concert by The Bangles.
Rory and Dean disagree about women's roles after watching "The Donna Reed Show."
Rory's father, Christopher, returns, causing tension in Emily and Richard's house--and forcing Lorelai to make a big decision about her family's future.
Dean and Rory share a special evening as the town celebrates its romantic history.
Dean ends his and Rory's relationship on the night of their third anniversary. Refusing to indulge in self-pity, Rory attends a party and finds her classmate Tristin, who just lost his girlfriend. When Tristin kisses Rory, she finally admits to herself how confused and miserable she is. Meanwhile, Lorelai visits Max, and the two can't resist making love.
Emily becomes worried when Lorelai's grandmother offers Lorelai a trust fund for Rory's education. If Lorelai accepts the trust fund, Emily fears she will lose contact with Lorelai and Rory once they are not financially dependent on her. Meanwhile, Rory feels uncomfortable near Tristin after their kiss. She tries to pair Tristin with Paris, not realizing that she herself is the one whom Tristin is interested in.
Aghast to finally see the conditions in which Lorelai reared Rory instead of living with Richard and her, Emily tries to create the perfect bedroom for Rory in her house. Lorelai convinces Luke to give his former girlfriend a chance to reconcile with him.
Still upset over Dean, Rory becomes angry with Lorelai, who didn't tell her that she is dating Max again. Dean tells Lorelai that he left Rory because she couldn't say "I love you," and Lorelai urges Rory to express her emotions more freely.
Rory finally tells Dean that she loves him. Rachel senses that Lorelai and Luke are attracted and leaves town rather than pursue Luke anymore. Max also senses the attraction, which Lorelai denies. When Max proposes marriage to Lorelai, she is caught off guard and rebuffs him saying he should have done it the "right" way with 1,000 daisies and a white horse. The next day, Lorelai arrives at the inn to find it full of daisies. Again, Max proposes marriage, and Lorelai considers her response...