When Rory gets accepted into Chilton, Lorelai has to deal with the fact that she can not afford the school and must go to her parents for help. Her parents, Emily and Richard, help her out by providing a loan to pay for the school, but in return ask that her and Rory must attend dinner every Friday night at their house. During her last couple of days at Stars Hollow High, Rory meets a new transfer student, Dean, and begins to reconsider her transfer to Chilton. When Lorelai sees that Rory is thinking of giving up her future for a boy, she becomes angered and they engage in their first fight ever.
It is the first day of Chilton for the Gilmores, and Lorelai oversleeps. Realizing that she does not have enough time to pick up her clothes from the dry-cleaners, she is forced to wear a pink tie-dye shirt and 'Daisy Duke' shorts, an outfit that upsets both Emily and Rory. The rest of the day is downhill from there for Rory, who picks up the nickname Mary and makes enemies with Paris Geller who sees Rory as her competition.
Rory joins Richard for a round of golf at the club, finding that she enjoys spending time with her grandfather. When Rory returns from her day at the club, Lorelai is not to happy about the fact that Rory may want to be a part of the world she ran away from, resulting in her picking a fight with Rory. Meanwhile, Lorelai helps plan a wedding for a set of twin girls who are marrying a set of twin boys.
At school, Rory receives her first D ever, leading her to study like crazy for the upcoming exam. After she and Lorelai spend all night reviewing Shakespeare, they oversleep. To make matters worse, on her way to school Rory hits a deer which further delays her arrival to Chilton. When she finally makes it to school, she is denied from taking the test and does not handle it well. Lorelai is called in, and tells off the headmaster and Mr. Medina.
At the Chilton bake sale, Lorelai runs into Mr. Medina and agrees to have coffee with him. When they get together, he insists that they should date, and Lorelai agrees to go to dinner with him. But when Lorelai receives a call from Rory saying that their neighbor's cat, Cinnamon, had died, their date slips her mind as she helps prepare for the wake. During the wake, Rory walks outside to see none other than Mr. Medina outside on her porch, waiting for Lorelai. Later at the wake, Rory has an awkward encounter with Dean who admits his feelings for her.
It is Rory's 16th birthday and both Lorelai and Emily have planned parties for Rory. At Emily's, all of Rory's classmates are invited leading Rory to have her first fight with Emily. The following day, Lorelai throws Rory another bash and Emily and Richard decide to attend hoping to reconcile with Rory. However, while at the party, both Emily and Richard realize how different Rory and Lorelai's lives are from their own. Later, Dean comes by once everyone has left to give Rory a bracelet he had made for her. As they hold hands in the yard, Lorelai oversees.
Dean and Rory share their first kiss, but Rory decides to hide the news from her mother. When Lorelai hears about the kiss from Mrs. Kim, she tries to prove to Rory that she's okay with Dean by inviting him to join their movie night. There, Lorelai lays down the law when it comes to dating her daughter.
The first snow of the season hits Stars Hollow -- Lorelai's favorite time of year. The roads ice over and Rory is forced to stay with her grandparents where she introduces them to the wonders of frozen pizza. Back in Stars Hollow, Lorelai runs into Max, whose car had died on his way home. Since he's stranded in Stars Hollow for the night, Lorelai takes him out to dinner and a movie, but their date is cut short when they find Lane at Lorelai's, waiting for Rory. Later, Rory returns home and is shocked to find her teacher asleep on the couch.
Rory asks Dean to the Chilton formal despite reluctance to do so. While making Rory's dress, Lorelai throws her back out and Emily, noticing the pain she's in, insists that she stay with Lorelai while Rory's at the formal. At the dance, Dean has an encounter with Tristan that leads to a fist-fight between the two. After the dance, Rory and Dean fall asleep together while reading as Miss Patty's. The next morning, Lorelai wakes up to the angry voice of Emily and finds that Rory has not returned home.
Lorelai and Rory's relationship is still a little rocky from the night of the dance, as is Emily and Lorelai's relationship, causing Rory to go to the elder Gilmore's Christmas party alone. While Rory is at dinner, Dean and Lorelai are able to work things out, and Lorelai ends up spending her evening with Luke who makes her a festive 'Santa Burger'. However, their evening is cut short when Lorelai gets a frantic call from Rory that Richard collapsed. With emotions running high, Lorelai finds it hard to visit her father and leans on Luke for support. Later, Rory and Lorelai reconcile their differences when they see just how valuable life is.
Lorelai and Max's relationship begins to become more serious, but Lorelai begins to back out when she sees how much Rory likes him being a part of their lives. At Parents' Day, Lorelai tries to break up with Max, but they end up kissing while Paris watches in the doorway. In order to get the school's mind of her parents' bitter divorce, Paris exposes Max and Lorelai's relationship, much to the horror of Rory. Meanwhile, Sookie asks Jackson out.
After helping Sookie to ask Jackson out, Lorelai finds out that the only way for Jackson and Sookie to go out is for Lorelai to go with them on a double date. Lorelai reluctantly accepts, ending up with the date from hell -- Jackson's cousin Rune. Meanwhile, Rory and Lane double date with Dean and his friend Todd without telling their mothers where they actually are. Later, Luke finally gets up the courage to ask Lorelai out, but Mrs. Kim interrupts when she cannot find Lane.
Lorelai heads up the Stars Hollow Charity Rummage Sale and ends up buying a sweatshirt that Luke donated. When she wears it around town, Lorelai is bewildered when Luke is angry to see it. Later, Sookie reveals to Lorelai that the previous owner of the sweatshirt was Luke's first serious girlfriend. Meanwhile, Sookie is given tickets to the Bangles concert in New York and Rory invites Madeline, Paris, and Louise to go with them to New York. At the concert, Madeline and Louise end up leaving to go to a party, much to the horror of Lorelai.
It is The Donna Reed Show night at the Gilmores, and Dean tells the girls that he thinks the idea of a wife cooking and cleaning for her husband is nice, which doesn't go over too well. The next day Rory comes home with a bird, who turns out to be her mid term project. She is asked to babysit Babette's new kitten, leaving Lorelai with her bird. At Babette's, Rory thinks about her fight with Dean then decides to cook dinner and dress like Donna Reed to make up. Lorelai arrives back home, she finds that the bird has escaped, and calls Luke to find it. Meanwhile, an unexpected visitor reappears in Lorelai's and Rory's life.
Christopher returns to make up for lost time with Rory, and Emily, elated about his return, invites both Christopher and his parents to Friday Night Dinner. But tensions between the Haydens and the Gilmores rise, resulting in a fight about Lorelai and Christopher's past. After the fight, Lorelai goes to her old room, to find Christopher on the balcony and old romances are rekindled. The next morning, Lorelai realizes she forgot about Luke and the paint, and apologizes. When Lorelai returns home, Christopher is waiting to ask Lorelai a question.
A woman from Luke's past comes back to Stars Hollow, and tells Luke that she is here to stay. Rory misses Friday night dinner to go on a three month anniversary date with Dean. At Friday night dinner, Emily tries to set Lorelai up with a family friend, much to Lorelai's disgust. Meanwhile, Dean surprises Rory with a fancy dinner, then shows her a car that he's building for her. But the night takes an unexpected turn when Dean tells Rory he loves her and Rory doesn't answer him back.
Now broken up with Dean, Rory decides to take her mind off of the break-up by making lists and not listening Lorelai's advice to wallow. After being invited to a party at Madeline's, Rory decides to go and Lane tags along. However, things take when Rory finds herself alone with Tristan, who also just broke up with his girlfriend and is in need of consoling. Meanwhile, Lane meets a Korean boy.
Emily is upset when she finds out that Richard's mother, Trix is coming by for a visit. Meanwhile, Paris is not pleased that Tristan asked Rory out on a date. When Paris talks to Rory about it, she denies it, making Paris even madder. During Friday night dinner, Trix offers to help Lorelai and Rory, but Emily, afraid of losing Lorelai and Rory, warns Trix not to.
Rachel discovers an abandoned inn and shows to Lorelai, who immediately falls in love with it. Meanwhile, Rory takes Emily on a tour of Stars Hollow where immediately befriends Mrs. Kim and Michel, but becomes upset when she sees Lorelai and Rory's first home. Lastly, Lorelai gives Rune a job at the inn as a favor to Sookie.
Lorelai helps Luke buy a birthday present for Rachel, but ends up buying him a new wardrobe along the way. Still upset over the fact that she and Dean broke up, Rory becomes very upset when she finds out that Lane and Dean are science project partners, and then becomes angered when she finds out that her mom and Max have gotten back together. She and Lorelai fight, and Rory runs away to her grandparent's house in Hartford. Wanting to hear the whole story about Dean and Rory's break up, Lorelai talks to Dean and hears what happened on their anniversary date, worrying Lorelai that Rory has the same commitment problem as she does.
Rachel leaves Stars Hollow when she realizes who Luke really has feelings for. Luke and Max have an argument over Lorelai, making Max think that he and Lorelai dated. Meanwhile, Rory defends the town troubadour, which brings her and Dean together, and finally says 'I love you'. Max, wanting to show Lorelai that he was serious about his proposal, surprises her with 1000 daises and asks his life-changing question again.