Lorelai confesses that part of the charm of breakfast by Luke is breakfast at Luke's; Rory is less than thrilled to discover that the common room in her suite has been overtaken by a huge antique printing press Paris inherited from Asher; Lorelai and Sookie head up Jackson's campaign committee when he decides to run against Taylor for town selectman to put an end to the grocer's petty tyranny over Stars Hollow, but Lorelai has second thoughts when she sees how Jackson's projected landslide victory is affecting Taylor; Rory and Dean have difficulty finding a comfortable place to be alone, compounded by Dean's having to share a car with Lindsay and his reluctance to make his relationship with Rory public; Lane confesses her true feelings to Zack; after all the votes have been counted, Jackson isn't quite certain he wants the job, and Taylor vows not to go away quietly.

Rory forgives Logan, then needs some time for herself, so she pays a visit to Lorelai in Stars Hollow. 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. And, against Lorelai's wishes, Rory pays a visit to the store owned by April's mother, Ana, to spy on her. 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.

Lorelai wakes up next to Christopher after she breaks-up with Luke. Rory receives a model rocket as a going-away present from Logan and struggles to decode its significance. Kirk crashes into Luke's diner. Luke tries to get Lorelai back, but she informs him that she slept with Christopher. Christopher calls Lorelai and says, "That other night was incredible and I hope it can happen again." Lorelai replies, "That night was a mistake and it cannot happen again."

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.

Lorelai and Chris fly to France to take Gigi to see her mother, Sherry. Once there, Chris proposes to Lorelai and the couple return to Stars Hollow as Mr. and Mrs. Hayden. The joy of Rory's trip to the country (Stars Hollow) with Lucy and Olivia is dampened by Rory's breakdown regarding her fears for the future, and the unexpected appearance of a past friend who disavows having known Rory. Zach and Lane find out they're having twins and break the news of their impending parenthood to Mrs. Kim, with unexpected consequences.

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.

Luke asks Lorelai to be a character reference in his custody case. Rory comes back from London from Chirstmas with Logan, where she and Logan have made amends. The Gilmore girls celebrate Christmas a month late. April sneaks out to see Luke.

Richard is in the hospital with Emily, Lorelai and Rory in the waiting room; Logan comes to be by Rory's side. Lorelai calls Christopher to let him know, but cannot reach him. Luke hears about Richard and comes running to help.

Lorelai is having a hard time confessing her breakup to Emily but to her surprise encounters sympathy when she does. Rory prepares a "Gilmorish-birthday" for Logan to show him that a birthday can be fun as opposed to the way they get celebrated in the Huntzburger family. Logan learns that his company's patents aren't valid due to prior art.

Lorelai plans a road trip to attend the wedding of Mia, the woman who served as a surrogate mother/grandmother to the girls for years. Rory has a fight with Logan over his immature reaction to his business disaster, and agrees to go on the trip with Lorelai. 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. Lorelai learns that Emily came to see Mia five years earlier to ask for pictures of Lorelai and Rory during the years they were estranged. Logan makes a surprise appearance and asks Rory to forgive him. Meanwhile, Lane and Zack ask Luke to be the godfather to their twins Steve and Kwan. Finally, Lane goes into labor and Luke helps get everyone to the hospital.

Lorelai tries to reacquaint herself and Luke by visiting the diner, but the reunion results in an awkward silence. Paris freaks out over too many opportunities when she gets accepted to a quite a few graduate programs. Rory's hopes get squashed when she gets rejected for the internship at the New York Times. While staying with Lorelai, Jackson accidentally destroys her dollhouse.

At Rory's graduation party at her grandparent's house, Logan proposes to her. Emily and Richard sing Rory a graduation song. Rory is caught off-guard and says she needs time to think about it. After Rory graduates from Yale, she tells Logan that she can't marry him. Logan tells her it's all or nothing and Rory decides to decline. Logan ends their relationship.

Rory lands her dream job as a political reporter in Ohio. Luke enlists the help of everyone in Stars Hollow to throw her a graduation party in order to say goodbye. Luke's thoughtfulness brings out a long-awaited reaction from Lorelai.