Lorelai Gilmore has made her share of mistakes in life, but she has been doing her best to see that her college-bound daughter Rory, who’s also her best friend in the world, doesn’t follow in her footsteps. That may be easier said than done, considering that the two share the same interests, the same intellect, the same coffee addiction and the same eyes.
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.
Lorelai decides that a double date with Rory and Dean is the way to smooth over the bumps in her relationship with Dean, but the evening quickly goes awry.
While Rory plays spy for her grandmother at her new job, Lorelai can't decide on a date for the wedding.
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.
During their weekly dinner at Emily's, Lorelai learns of her cousin's funeral. The next day Rory reminds Lorelai of the Chilton bake sale where Lorelai accepts to meet Max Medina, Rory's teacher, for coffee. Rory's friendship with Dean takes a new turn.
The magazine comes out and Luke and Lorelai get a little too enthusiastic when celebrating. Rory is given a surprising review by Mitchum Huntzberger.
After months of separation, Sookie tries to reconcile Rory and Lorelai by asking them to be the godmothers of her two children. However, they both end up fighting when Lorelai realizes that Rory didn't see fit to share her new cell phone number with her.
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.
Lorelai discovers Luke's secret and is distraught by his reaction. Logan tries to get Rory back.
Lorelai begins to wonder if all the choices she's made have been due to her trying to rebel against her mother. Christopher tells Lorelai that he loves her.
Rory organizes a fabulous D.A.R. party for Emily but the evening doesn't turn out so well when Richard confronts Mitchum Huntzberger, Logan's father, about his opinion on Rory's journalistic talents. Emily and Richard find out Lorelai was right about Logan's parents.
Rory's application for Harvard arrives, plunging Rory, Lorelai and Emily into a frenzy. Taylor steamrolls Luke into opening a soda shop next to the diner. Lane places an ad in the paper for a band and finds a musical soulmate. Dean has a talk with Rory about their future after she goes to Harvard.
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.
Lorelai and Sookie head up Jackson's campaign committee when he decides to run against Taylor for town selectman. Rory and Dean have difficulty finding a comfortable place to be alone to clear up their relationship.
Lorelai and Chris fly to France to take Gigi to see her mother, Sherry. Zach and Lane find out they're having twins and break the news of their impending parenthood to Mrs. Kim, with unexpected consequences.
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.
Spurred on by her editor, Rory writes a strongly opinionated dance review that leads to a dining hall confrontation. When she learns that Nicole and Luke have put their divorce on hold and have resumed dating, Lorelai becomes so flustered that she has an argument with Luke.
Lorelai finds herself on the double date from hell with Jackson's very odd cousin after offering to help ou Sookie. Meanwhile, Rory and Lane get into trouble when they double date with Dean and his friend Todd without telling their moms.
Christopher begins to doubt Lorelai's feelings for him when he witnesses Luke and Lorelai sharing a moment. Logan discovers that Rory and Marty have been pretending that they just met, and he reveals the truth to Lucy. Emily gives Lorelai advice about her marriage.
Rory is angry that she could not attend Lorelai and Chris's wedding. Logan is moving from London to New York City. He and Rory fight about an article she wrote. April develops appendicitis and Luke takes her to the hospital.
Rory receives a strange going-away present from Logan and struggles to decode its significance. Luke tries to get Lorelai back, but a unwelcome night's event forces Lorelai to brush him off.
Chris and Lorelai tell Emily and Richard about their marriage. Anna tells Luke that she is moving across the country and taking April with her, in which Luke tells Anna he will fight for custody. Rory moves in with Paris, after moving out of Logan's apartment.
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.
After Rory isn't able to go on the trip to Asia with Logan, Lorelai throws her an Asian-themed party. Lane and Zach return from their less-than-perfect honeymoon in Mexico. Luke and Lorelai begin to deal with their break-up.
As The Gilmore face a crisis, Lorelai tries in vain to contact Christopher, as Logan and Luke come by their side to offer support.
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