Tension is still thick between Rory and Lorelai over Dean, so Rory seeks out Lane's perspective and decides to talk to Dean, which leads to more trouble. Lorelai and Luke clarify their new relationship while Emily announces she and Richard have separated. She and Rory decide to head to Europe to escape their problems.
With Lorelai & Rory's relationship still strained and unresolved, Lorelai takes on everything at the inn till Sookie convinces her to take some time off. At the corner of bark and cheese, Rory realizes she was wrong and writes Dean a letter which she asks her mom to deliver. Lane begins to see Zack in a new light and Lindsay finds Rory's letter which leaves Dean out in the cold and without either girl.
Luke and Lorelai enjoy their first official date where Luke tells her he's all in for their relationship. Their new relationship is the basis for the next town hall meeting. Paris has a wake for the passing of her boyfriend and Rory meets a new guy.
Fed up with all the hoops Taylor makes Jackson go through, Jackson decides to run for town selectman with Lorelai and Sookie heading up the campaign only to find that he may not want the job after all. Rory and Dean try to work things out, but have trouble finding a place to be together.
Jackson is overwhelmed by the demands of his new job while Lorelai and Rory decide to see if they can get Richard and Emily back together. With Dean back in the picture, Lorelai tries to make things right with dinner and a movie, but when Pippi Longstocking isn't a good enough distraction for Luke's feelings that Dean isn't good enough for Rory, Lorelai has to bring out the Bop It!.
Rory, desperate for a story idea for the Yale paper, finally decides to research and write about a secret Yale society which happens to have connections to Logan. The Dragonfly Inn's accountant suggests dropping the lunch menu till the money situation improves, which has Sookie upset with the regularly lunching Norman Mailer, who only orders ice tea. With Luke and Lorelai hitting it off, Rory asks her dad to stay out of the picture. Sookie realizes she's pregnant again.
When Emily discovers that Lorelai is dating Luke, she insists he come to dinner. Not to be outdone, Richard invites Luke to a game of golf, and Luke finds himself overwhelmed by the strength of the elder Gilmores' personalities.
Luke tries to smooth things over with Liz and TJ when they stress out about buying a house in Stars Hollow. When Emily learns Rory and Dean are dating again, she calls a temporary truce with Richard to throw a party to introduce Rory to more suitable men. Dean realizes he isn't one of them, and Logan realizes he is.
Jackson has his hands full between Sookie's food cravings and his town selectman duties. Lorelai invites Christopher to lunch, but Rory tells him off and asks Lorelai what Luke thinks of her and Christopher having lunch. Emily decides she's still a viable commodity and asks Lorelai to help her start dating.
Rory is asked to host a Chilton student for a few days at Yale, but the student is more interested in her freedoms than the responsibilities that go with them. Lorelai learns about Luke's dark day, which happens to fall on the same day as Miss Patty's 40th anniversary party. Logan works his way into Rory's life, prompting her and Richard to pull a little prank of their own.
After finding out that Emily started dating again, Richard's jealousy forces him to reconcile and they both agree to renew their wedding vows. Rory offers to help Logan with an article and Emily lets Christopher know Lorelai and Luke are getting serious.
Emily and Richard renew their vows. Rory experimentally kisses Logan, triggering a turf battle between Luke and her father Chris, who insists that Lorelai's attachment to Luke is temporary, because Emily has convinced Chris that he and Lorelai are meant for each other.
After all the drama at the wedding, Lorelai is afraid she'll lose Luke, who needs time to process what's happened and finally decides her family and history may be too much for him. She takes to her bed to wallow where Rory tends to her needs while the town takes sides.
Lorelai is hurt again when she realizes Luke has moved his boat from her garage without even telling her. Luke helps the school kids build the sets for their Fiddler on the Roof play in hopes of working with Lorelai who he is realizing he misses. Rory tries to make up with Marty by hosting a movie night, but Logan interferes.
Luke, upset and missing Lorelai, begins to take it out on his customers. Lane realizes her mom is in her head, and with the grandparents back from their second honeymoon Rory makes it clear that Friday night dinners are just dinner and nothing more. Emily acts like she doesn't realize all the hurt she's caused Lorelai, but goes to see Luke to make things right.
Rory and Logan's casual dating situation gets more complicated when Rory spots Logan with another girl and her jealousy sets in. Rory decides to go to a party with a guy she barely knows, which makes Logan jealous. Luke and Lorelai resolve things, but Lorelai is still upset with her mom and refuses to go to Friday night dinners, which makes Emily wonder if Luke followed through on their previous discussion.
Luke volunteers to help convert old man Twickum's house into a museum just to see if he can buy it. Meanwhile with the help of some Founder's day punch, Lane, Paris and Rory commiserate about their love lives. Lorelai forgets to keep some news off the record when she is interviewed by a magazine about the success of the Dragonfly Inn.
After realizing that casual dating isn't for her, Rory tries to break things off with Logan, causing him to agree to see her exclusively. Logan's family isn't happy about the match despite Rory's breeding. Luke's patience is tried as he takes over as temporary chef at the Dragonfly while pregnant Sookie is ordered to bed rest, but Sookie has trouble giving up control of her kitchen. Meanwhile, Paris finds out where Doyle has been all weekend.
Taylor agrees the museum is a bust. Lorelai meets to discuss selling the Dragonfly while Rory starts her new internship with Logan's father. Friday night dinner with the grandparents goes great for Logan and Rory while Lorelai, after begging to attend, gets the cold shoulder.
The article about the Dragonfly comes out and Luke and Lorelai celebrate. Sookie goes into labor. Logan's dad Mitchum reviews Rory's work and Luke has competition from an unlikely source to buy the Twickham house.
Rescuing Rory after a night of reckless behavior with Logan, Lorelai is shocked to hear her daughter's plans for the future. Lorelai first turns to Richard and Emily for help, but soon realizes that Luke is the only person she can trust.