The first snow of the season falls heavily, stranding Rory at Emily and Richard's house. Luke is obsessing about the silliness of the re-enactment of the Battle of Stars Hollow in the town square. Lorelai is enjoying a walk alone in the snow when she comes upon Max. Lane decides to pay a visit to Rory.
Rachel finds an abandoned inn that Lorelai and Sookie fall in love with. Rory takes Emily on a tour of Stars Hollow. Emily hits it off with Mrs. Kim and Michel, but becomes distraught when she sees Lorelai and Rory's first home. At Sookie's urging, Lorelai gives Jackson's cousin Rune a job at the Inn.
Lorelai helps Luke shop for a birthday present for Rachel. Meanwhile overwhelmed by sadness at her breakup with Dean, Rory is distressed to discover that Lane and Dean have become science project partners, and incensed to find out from Max that Lorelai has neglected to mention that they are dating again.
To escape everyone's reaction to the news of the broken engagement, Lorelai and Rory hit the road, and stumble upon the bed and breakfast from hell. Rory gets a taste of college life while visiting Harvard and Lorelai muses over what might have been. Lorelai decides to get serious about making her dream of opening an inn a reality.
A blizzard prevents a group from attending the historical dinner that Sookie has painstakingly prepared at their request, so she and Lorelai invite most of the citizens of Stars Hollow to an elaborate feast complete with Elizabethan costumes and horse-drawn sleigh rides. Rory struggles to keep the budding rivalry between Dean and Jess under control.
When Dean notices that Rory isn't wearing the bracelet he made for her, she covers her shock at its loss and lies that she removed it because of a rash on her arm. She searches for it frantically all over Stars Hollow, not realizing that Jess picked it up after she dropped it on the bridge two weeks earlier.
When Emily and Lorelai go to a spa for a weekend of relaxation, Emily ends up bonding with Lorelai in a way that only her daughter could inspire. Thrilled that she has the house all to herself, Rory hopes to spend a quiet night at home doing laundry and eating Indian food but her plans are foiled -- first by Paris, then by Jess, and finally by Dean.
Christopher shows up uninvited at Friday night dinner and quarrels with both Lorelai and Rory before Emily asks him to leave. Rory runs into Jess and they each betray their hurt feelings. Francie targets Paris and Rory for a world of trouble if Rory doesn't stop Paris from running the student council like a dictatorship.
Lorelai's stint in the Stars Hollow High School local business success speakers forum gets derailed by some controversial personal questions, much to the delight of Luke and the consternation of some PTA mothers. Lane alleviates her frustration about the strictures of her household and the future of her band through a colorful display of independence.
Lorelai chauffeurs Rory to Sherry's baby shower in Boston and finds herself dragged into the festivities against her will. Jess comes home with a car and Luke tries to find out where he got the money to pay for it. One of Stars Hollow's more eccentric citizens requests a permit to mount a demonstration in the town square.
In the aftermath of the Dance Marathon, Kirk parades around Stars Hollow with the trophy until someone steals it, while Lorelai and Rory painfully inch their way towards Luke's. Lorelai and Rory reluctantly agree to accept Richard's invitation to accompany him and Emily to his Whiffenpoof reunion at Yale.
It's Thanksgiving, and Lorelai and Rory have dinner at four different places: the Kim's, where Lane has managed to get Dave invited; Luke's, where Luke and Jess make it a foursome with Lorelai and Rory; Sookie's, where Jackson and his family have deep-fried the turkey, the lawn and just about everything else; and Emily and Richard's, where, to Lorelai's horror, Rory reveals that she has applied to Yale.
Lane's clever scheme to get her mother's permission to attend the prom horribly backfires. Luke offers to teach Lorelai the fine art of fishing after Alex invites her to go fishing. Paris' and Rory's conflict is brought to a swift end by Headmaster Charleston, who threatens to revoke the glowing letters he wrote to Harvard for each of them.
A fire at the Independence Inn forces Lorelai to relocate its guests. Sookie invades Luke's with staff in tow to prepare breakfast for the Inn's guests. Questions arise about Jess's attendance at school when he receives the Employee of the Month award from WalMart. Lorelai and Rory start picking up on weird and somewhat unfriendly vibes coming from Nicole and Lindsay.
To help meet the expenses of opening the inn, Lorelai and Sookie decide to become caterers on the side, with their first assignment being a "Lord of the Rings" theme party. At Yale, Rory returns from class to find that Emily has redecorated the apartment. Meanwhile, Richard ponders a proposal to take on a new business partner.
Rory accepts a classmate's invitation to go out on her first date since breaking up with Jess, while her roomates engage in a war of wills. Lorelai invites Luke over to share the traditional Gilmore movie night she used to have with Rory, although she is somewhat disturbed after discovering that the designer she just hired to decorate the inn used to work for Emily.
Jess's attempts to keep a low profile but keeps bumping into Rory all over town. Emily is in a dither about filling a table at a benefit and enlists the help of Lorelai and Jason, whom she encourages to pretend that they're a couple. Luke is less than impressed by Liz's latest business venture and newly-arrived boyfriend.
Liz returns to Stars Hollow to announce that she's getting married in the town square in a week. Rory tries to hide her discomfort when Lorelai tells her about overhearing a fight between Dean and Lindsay. A self-help tape helps Luke clarify his thinking, and a talk with Jess gets him started on the path to having the relationship he's been looking for all along.
Luke volunteers to build the sets for a school production of "Fiddler on the Roof," knowing that Lorelai is doing costumes, in hopes that their paths will cross. Meanwhile, at Yale, Rory plans to reconnect with Marty to watch Marx Brothers movies, but Logan interrupts their day by inviting them to dinner with his group.
When Richard and Emily return from their second honeymoon, Rory attends Friday-night dinner without Lorelai, who refuses to speak to her mother or see her, and plans a girls' night out with Sookie instead. Meanwhile, Luke, who's miserable without Lorelai, takes his anger out on his customers. Meanwhile, Lane has a horrific realization about her mother's inluence.
Feeling a little lonely, Lorelai adopts a dog. Luke agrees to repair Lorelai's house, rather than buy the Twykham house. Rory starts her community service assignment. Feeling neglected and unhappy with how things are going, Rory visits Luke at his diner. He lets it slip that he and Lorelai are engaged, leaving Rory feeling even more alone.
Both Rory and Lorelai are saddened by the fact that their estrangement is keeping them apart on Rory's 21st birthday. Emily takes it upon herself to plan a party for her granddaughter when Rory shows no interest in the event. Lorelai tries to convince Luke to participate in her mad scientist Halloween skit.
After a long absence, Christopher reappears in Lorelai and Rory's lives. Lorelai and Rory enjoy their first Thanskgiving at the Dragonfly Inn, and Rory receives surprising news about Logan. On the eve of an important gig for the band, Lane has to deal with Zach's jealousy over a song Brian wrote about her. Luke struggles with his life's new development.
While Luke deals with the reality of having April in his life, Lorelai tries to pretend she doesn't mind the repercussions the new situation is having on their engagement. Rory's concern over Paris' lack of management skills at the Yale Daily News finally reaches a crisis point. The subsequent Friday night dinner erupts into an emotional confrontation where all four Gilmores finally get their issues out on the table.
As Valentine's Day approaches, Rory and Logan invite Lorelai and Luke to spend a weekend with them at Logan's family's house on Martha's Vineyard. Lorelai is upset at Luke's attitude towards Logan until an unexpected event bring the two men closer. When Lorelai finally confesses to Luke that she is worried the wedding will never take place, he reassures her that they will get married soon.
Lorelai offers to help Christopher out by babysitting his 4-year-old daughter, G.G, and is horrified by the toddler's terrible behavior. The next day, Rory and Logan attend the wedding of Logan's sister, Honor. While helping the bride and her three bridesmaids get ready, Rory is devastated to learn how Logan spent his time during their recent breakup.
Although Lorelai refuses to admit that she is upset, Rory can tell that she is bothered by the news that Luke will be gone for a few days on a field trip with his daughter, April. Meanwhile, when Zack finally works up the courage to ask Mrs. Kim for permission to marry Lane, he is surprised at the deal she makes with him.
Although Rory and Logan are back together, Logan is miserable knowing that Rory hasn't really forgiven him, and he takes off with his friends for another stunt with the Life and Death Brigade. Rory accepts Jess's invitation to attend an open house at his new book store/art gallery/publishing house in Philadelphia. While there, she is surprised to run into Luke, who is accompanying his daughter April on an academic field trip.
Luke decides to give April a birthday party at the diner. Lorelai volunteers to help, and is hurt when Luke explains that he still thinks it's too soon for April and Lorelai to meet. Meanwhile, Rory rushes to be with Logan at the hospital after he is seriously injured during a stunt with the Life and Death Brigade.
Logan returns to town on business to acquire an internet company and pays Rory a surprise visit. Rory is thrilled but, during a dinner with Logan's colleagues, realizes that she has no connection to his new business world. Lorelai and Christopher fight about Gigi going to Paris to be with Sherry for a few months.
Lorelai and Chris attend Yale Parents' Weekend where they find Emily and Richard. Chris takes Rory and all her friends out for dinner after feeling guilty that he wasn't around when Rory was growing up. At the end, she shows her commitment to her duties as editor of the newspaper by gathering the troops to report on a story.
Lorelai and Rory plan a road trip to attend Mia's wedding. Emily invites herself along in an effort to get away from Richard, who is driving her crazy while he recuperates at home. At the wedding, Emily is upset by the close relationship Mia shares with Lorelai and Rory. Finally, Lane goes into labor and Luke helps get everyone to the hospital.