Emily offers Lorelai and Sookie the job of catering the party to launch Richard's new business venture, then runs them ragged with demands. Meanwhile, at school, Rory finds that her roommates' activities are preventing her from studying.

Sookie and Jackson decide to have a home birth and enlist the services of a formidable midwife; when Stars Hollow mounts a festival of living pictures, Kirk goes way overboard in getting into character for his role as Jesus in ""The Last Supper"", while Lorelai has a bad case of stage fright; Lane, Zach, and Brian finally find an awesome guitarist to replace Dave, but wonder if he isn't too old to join the band; Nicole asks Luke if they can postpone the divorce and start dating again; Jackson's brother Beau, who's come to provide moral support during the delivery, is less than enchanted with Stars Hollow, and is right behind Sookie in expressing extreme frustration with the tardiness of the baby's arrival; as he escorts Lulu through town, Kirk proudly and repeatedly reminds everyone in Stars Hollow that he has a girlfriend.

Momentous changes are in the air as: the Dragonfly Inn approaches opening day by having a shakedown weekend; Rory and Dean take a major step forward in their relationship, to Lorelai's dismay; Emily and Richard admit that they're separated; Kirk decides to let Lulu in on the deep, dark secret of his night terrors; Jason appears at the Inn to plead his case with Lorelai, to no avail; Luke answers Lorelai's question about the status of their relationship when he makes it passionately clear to Lorelai that they're dating, to which she enthusiastically agrees.

Things are still testy between Lorelai and Rory, and Rory's refusal to discuss the Dean situation causes Lorelai anguish; Emily announces that she and Richard have separated; Sookie is ecstatic when Kirk tells her that Luke and Lorelai kissed; Rory's attempt to meet Dean and discuss what happened leads to a lot of action, but no talk; Dean provokes an argument with Lindsay after leaving Rory's house; Emily decides to go to Europe and invites Rory to accompany her; Lorelai and Luke are very tentative with each other the day after until they are able to reassure each other that they're on the right path; Luke heads off to Maine for a week to help Liz and T.J. with their Ren Faire booth; Rory decides that she needs a break from both Dean and her mother, and decides to take her grandmother up on her invitation to go to Europe.

The demands of the electorate are beginning to get to Jackson; Lorelai and Rory delicately nudge Richard and Emily closer together; 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 goes awry when Luke can't get over feeling that Dean isn't good enough for Rory; Richard takes up a new hobby, and Emily buys a panic room; failing to get a response from Zack about the declaration of her feelings, Lane rescinds them, which finally gets Zack talking; Lorelai introduces Luke to ""Pippi Longstocking"" as Kirk gets much better acquainted with Lulu during movie night at the Black & White & Read Bookstore.

Wanting to make peace with Rory, Christopher shows up at Yale, but she brushes off his attempt at compromise. When Lorelai learns that Christopher's father dies, she spends the evening at his place trying to comfort him, then disdains to tell Luke the truth about where she was. Also, Emily & Richard are briefly reconciled when they find and take in a lost dog.

Still smarting from her split with Luke, Lorelai is further stung when she notices that Luke has moved his boat. Meanwhile, 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 (Wayne Wilcox) to watch Marx Brothers movies, but Logan interrupts their day by inviting them to dinner with his group.

Now that Luke and Lorelai are back together, Lorelai can come into the diner, and she adds herself to Luke's speed dial. They make a date for Sunday to celebrate getting back together. Meanwhile, Kirk has stationed himself at the diner and is collecting the pink and blue ribbons which citizens of Stars Hollow used to wear. Rory and Logan are still dating, however not exclusively. Rory and Lorelai see him with another girl while they are shopping in downtown New Haven. Lorelai wants to go over and yell at Logan, but Rory informs her that it's OK - even though she doesn't look as if she really thinks it is OK. She tells Lorelai that they are just dating and allowed to see other people. Emily and Richard assume that since Emily gave instructions to Luke to get back together with Lorelai everything must be all set now. However, they are surprised to see only Rory show up for Friday dinner. They wonder whether Luke and Lorelai have gotten back together and end up assuming that Luke did

Lane and Zack's wedding is coming up and since Luke is busy, Michel is Lorelai's first choice as a date for Lane and Zack's wedding, but he gets Celine Dion tickets and bails. Rory suggests that Chris go as Lorelai's date and Chris is totally psyched to do it. Grandma Kim is a Buddhist and doesn't know that Mrs. Kim is a 7th Day Adventist. At Lane's wedding, Lorelai collapses and Christopher is there to take care of her.

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 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 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.

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.

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.