Lorelai is displeased that Rory has had sex for the first time with a still-married Dean. At the same time she is also happily reeling from her kiss with Luke, and both agree to keep their newfound relationship going. Meanwhile, Emily announces to the girls that she and Richard have separated and is wasting no time in heading off to Europe. Rory, conflicted over her night with Dean, decides to take up Emily's offer to accompany her to Europe.
Rory calls Lorelai while in Rome and opens up about how things really got out of hand with Dean. When she asks Lorelai to give Dean a letter she's written, Lindsay accidentally finds it and throws Dean out.
Waking up at Luke's place following a romantic night together, Lorelai accidentally walks into the diner wearing only a shirt and finds the diner packed with people.
Rory and Dean have a tough time being alone together due to the distance between their residences, which is complicated by the fact that Lindsay also has use of the car.
Lorelai tries to alleviate the awkward tension between herself and Rory over the Dean incident, but her plan to bring Luke on a double date with Rory and Dean go south when Luke is unable to hide his contempt for Dean. Meanwhile, Richard and Emily have a difficult time heading towards a reconciliation, despite the fact that neither knows what do with themselves without the other.
Lorelai and Sookie become ecstatic when they realize author Norman Mailer is continually showing up at the Dragonfly's dining room with a reporter in tow, but Sookie soon realizes that Mailer's not ordering anything to eat.
Rory agrees to go with Logan to one of his secret society goings-on, but she soon finds herself participating in an activity that is both exciting and incredibly dangerous.
Emily and Richard decide to throw Rory a party to get her acquainted with some of the Yale alumni, but after initially being moved, Rory is quickly disgusted to find out they are trying to match her up romantically with one of their kids.
Rory hatches a plan to keep the Friday night dinners with Emily and Richard going by getting herself and Lorelai to eat with them separately and coaxing the couple into getting back together.
Rory's old headmaster asks her to show around his daughter, Anna, who is interested in applying to Yale, but Anna is more interested in the partying than anything else, and ends up breaking off from Rory to discover college life on her own. Meanwhile, Luke and Lorelai have a huge argument after he learns that she has purchased a boat whose former owner was his father.
Christopher heads up to Yale, hoping to surprise Rory and perhaps mend his broken relationship with her, but his good intentions are refused. Lorelai learns of his father's passing and spends an evening trying to cheer him up, only she ends up keeping the truth hidden from Luke.
Rory is crushed when Logan reciprocates her help with his school newspaper article by not inviting her to be his date at a prestigious book-signing affair.
Lorelai throws Emily a bachelorette party on the eve of Emily's renewed wedding vow ceremony with Richard. At the wedding, Rory tells Logan of her desire for the two to start dating, despite his disinclination for a relationship, but the two are later found halfway-dressed in an intimate setting by Lorelai.
Following the Luke/Christopher confrontation at Emily and Richard's wedding, Lorelai tries to convince Luke to stick it out with her, but is crushed when he instead tells her he wants some time apart from her.
Lorelai becomes more despondent over Luke's absence when she finds his boat gone from her garage, bur Luke is planning to jumpstart communication between them when he agrees to build sets for an elementary school production of "Fiddler on the Roof" for which Lorelai is making costumes.
Richard and Emily return from their second honeymoon and resume the usual Friday night dinners, but Rory shows up alone, as Loreali refuses to forgive Emily for interfering in her love life, a sentiment which Rory bitterly echoes over dinner.
After spotting Logan with another girl, Rory wishes she hadn't said yes to the idea of dating other people. When Logan spots Rory at a Quentin Tarantino-themed party later that night with his friend, Robert, however, he comes clean about his discomfort with the arrangement.
When the home of Stars Hollow's oldest resident is left to the town following his passing, Luke decides to help out when the town readies to turn the house into a museum.
Rory decides to just be friends with Logan after realizing she is unable to have a fleeting romance with him, but is stunned when he tells her he wants to commit to her.
Rory tries to do extensive research on Logan's father before going to work as an intern at one of his newspapers. A curious Lorelai decides to call off her ban on Friday night dinners with Emily and Richard when she finds out they have asked to have dinner with Logan.
Rory gets a shock when she reads the first work performance review handed down from Mitchum Huntzberger. Luke suddenly finds that he and Kirk have competing plans to purchase the Twickham house. Meanwhile, Lorelai is ecstatic over The Dragonfly's inclusion in a travel magazine, but fears Emily will be critical of the article, Emily financially takes an aspiring ballet dancer under her wing, and Sookie's baby is on its way.
Lorelai comes to pick up Rory at a police station after a night of debauchery with Logan gone out of control, and is stunned to find out what Rory plans to do with her future. After asking Emily and Richard for help with the matter, she quickly learns that Luke is the only one to whom she can turn.