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."

Luke punches Christopher after finding out Lorelai slept with him. After not being able to go on the trip to Asia with Logan, Lorelai throws Rory an Asian-themed party, but Rory finds out that Lorelai slept with Christopher and gets upset. Lane and Zach return from their less-than-perfect honeymoon in Mexico. Lane reports to Rory that sex is overrated; learning that she is pregnant does not help her opinion. Luke and Lorelai begin to deal with their break-up.

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 begin to date. Christopher forgives Sherry after she sends him a letter apologizing. Rory returns to Yale for the fall semester of her senior year. April is staying with Luke temporarily while her mom, Anna, is out of town. Richard starts at Yale as a guest lecturer. Rory covers an art exhibition for the Yale newspaper and meets her new friends, Lucy and Olivia.

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. Christopher asks Lorelai to go to Paris with him.

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 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.

Chris and Lorelai tell Emily and Richard about their marriage. Lorelai becomes determined to make Christopher liked by the people in Stars Hollow. 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. She attends a party at Lucy's apartment; Marty reveals to Rory that he still has feelings for her. Luke's evident feelings for Lorelai are still apparent in his behavior.

Luke and Lorelai share a moment when Luke introduces her to Liz's new baby, and Christopher witnesses the scene. Lorelai and Christopher get into a fight over what Lorelai wants versus what Christopher wants. Luke contacts a lawyer over his custody troubles with Anna. Christopher and Luke fight in the town square. 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.

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.

Rory makes amends with Lucy while Christopher finds the letter Lorelai wrote for Luke's character reference. Rory witnesses a frightening sight while at Richard's Economics class. Sookie is acting weirdly so Lorelai makes Jackson confess: Sookie is pregnant again, even though Sookie told Jackson to get a vasectomy.

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.

Richard is feeling better and preparing to leave the hospital. Michel's dog Chin Chin dies and Michel guilts Lorelai into holding his memorial at The Dragonfly. Rory has a crush on the teacher's assistant that is filling in for Richard and confesses her "self-destructive" feelings to Logan. Lorelai and Christopher end their marriage after he calls her out on still having feelings for Luke.

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 and Rory throw Lane's baby shower, but Lorelai has to settle a fight between Lane and her mother first. Rory has an interview with the New York Times. Luke sells his father's boat to Kirk and buys a new and bigger one. Logan finally tells Rory about his business situation, and she tries to help out even though there's nothing she can do. She offers to come home from Lane's baby shower early to be with him, but Logan decides to go to Las Vegas with Colin and Finn to blow off some steam.

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.

When Taylor spends all of the Spring budget on a hay bale maze, it forces Lorelai and Luke to reunite while in the hay bale maze. Rory and Logan come to Stars Hollow for the Spring fair and Rory learns that she was given a job offer for a newspaper. When she evaluates what she truly wants she decides to reject the job offer and wait on an internship at the New York Times.

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.

After getting into a science camp, April tells Luke that she cannot go on the boating trip with him over the summer. Zach is asked to go on tour with another band. A drunk Lorelai serenades Luke at Karaoke night. Logan gets a job in San Francisco, where he then goes to Lorelai's home to ask permission to propose to Rory and take her with him. Lorelai, shocked, gives no answer.

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.