Picking up on the day after last season's finale, Lorelai wakes up in bed with Christopher. Confused and mortified, she makes a hasty exit, ignoring Christopher's pleas that she stay. Once at home, Lorelai tries to get rid of everything that reminds her of Luke and ends up practically emptying her house. Rory receives a toy rocket ship as a parting gift from Logan and is baffled as to its meaning. She decides she should join him in London for the summer, only to learn he has bought her a ticket for a visit at Christmas.
Rory is upset over Logan's absence and the fact that they had to cancel their long-planned trip to Asia. Wanting to cheer Rory up and take her mind off her own sad love life, Lorelai turns her house into an Asian-themed wonderland. Meanwhile, Lane returns from her disastrous honeymoon. While repairing the damage to the diner, Luke tells T.J. about his break-up with Lorelai. Finally, Rory is furious when she learns that Lorelai slept with Christopher.
When Richard and Emily have no real reaction to the news of her break up, Lorelai suddenly realizes that most of her emotional life has been based on doing and feeling the opposite of whatever her parents want. Later, when Michel forces Lorelai to attend Emily's cotillion dance, Lorelai discovers that some things her parents wanted for her weren't really that terrible. Meanwhile, Rory has a tough time making her long-distance relationship work.
Lorelai and Christopher have begun to date, and although Lorelai is finding it difficult to fully commit to the relationship, Christopher keeps coming up with romantic dates to win her over. Back at Yale, Rory meets some eccentric new girlfriends at an art exhibit, and Richard becomes a guest lecturer. April comes to stay with Luke for a few weeks while Ana is out of town. Finally, Emily gets arrested and Lorelai has to bail her out of jail.
Emily and Richard are delighted when Lorelai and Christopher attend Friday night dinner together as a couple. Christopher reveals that Sherry has written him a letter saying she regrets leaving their daughter, G.G., and asking him to send G.G. to visit her in Paris. Lorelai can't believe that Chris would consider this and they get into an argument over dinner. 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, she realizes that she has no connection to his new …
Christopher talks Lorelai into visiting Rory at Yale during Parents' Weekend, and Lorelai is surprised to find that Richard and Emily are also there. Trying to prove how cool he is, Christopher invites all of Rory's co-workers on the Yale Daily News to an expensive lunch where they all drink too much, and the meal ends abruptly when Rory insists they leave to cover a breaking story. Meanwhile, Luke meets April's swimming coach, who convinces him to take her adult swimming class. When the coach flirts with him, Luke asks her out on a date.
Christopher and Lorelai take his daughter Gigi to visit her mother in Paris. Despite severe jet lag, they manage to have a wonderful, romantic time enjoying the city and each other. Rory comes to the end of her tenure as Editor-in-Chief of the Yale Daily News and suddenly finds herself unsure of her future. Her new friends Olivia and Lucy suggest a trip to Stars Hollow for a girls' night. When they return, Rory is surprised to find that Lucy's new boyfriend is her old friend Marty, who pretends not to know Rory. Christopher and Lorelai return home with a surprise for …
Rory goes home to Stars Hollow to have dinner with her parents, where it is revealed that they eloped while in Paris. Rory pretends to be happy but later reveals her anger to Lorelai. Logan comes back to town for a launch party, which Rory attends and about which she later writes a judgmental article. Due to accusations by Logan, Rory plans to find a new apartment. Meanwhile, Luke turns to Lorelai in a time of medical emergency with April.
Here comes the birth of Liz's baby delivered by a midwife. Luke is informed of the news. A “knitathon festival” takes place in Stars Hollow.
Emily throws an extravagant party. Meanwhile, Luke talks to a lawyer about partial custody over April. Something big happens between Luke and Lorelai. “St. Nick might bring more than fruitcake this season.”
Lorelai and Christopher put the holidays on hold until Rory returns from London; Luke asks Lorelai to write a recommendation letter for his custody battle.
Noticing Sookie's recent odd behavior, Lorelai forces Jackson to tell her the reason. Luke and Anna attend a hearing to decide their custody battle over April. With help from Paris, Rory finally makes amends with Lucy, who tells her that she and Marty have broken up. While attending Richard's economics class at Yale, Rory witnesses a frightening scene. Finally, Christopher finds the letter Lorelai wrote for Luke's character reference and confronts Lorelai about whether he was her second choice.
Lorelai and Rory receive unexpected comfort and some grief while at the hospital and at Richard's side: Christopher won't return Lorelai's calls, but Luke is there for her and the family; Emily is so distraught that she tries to distract herself by maintaining her rigorous social calendar, with Luke offering to help her out in keeping up her appearances; Rory is met by Logan, who flies to the hospital in a helicopter; and, when Christopher finally does arrive, he speaks the words of sympathy to Lorelai, but his emotions betray him: he's still mad at her from their …
Rory quickly develops a crush on Richard's replacement TA and feels compelled to confess the attraction to Logan. But she feels really bad about it and he completely understands and the two of them reassure each other that in the end they are crazy about each other. Meanwhile, Lorelai distracts herself from thinking about Christopher by arranging a memorial service for Michel's dog. Christopher seeks her out, however, and the two are forced to face their problems. Christopher feels like he's been trying to get Lorelai to fall in love with him, and Lorelai realizes …
Lorelai puts off telling her parents about her separation from Christopher by helping Emily to arrange Richard's recovery. Rory celebrates Logan's birthday, but bad news from Logan's business partner spoils their evening.
Rory goes to meet with an editor from the New York Times, just as she starts to put together Lane's baby shower. Lorelai takes over the production and has to arbitrate a disagreement between Lane and Mrs. Kim about how to raise the unborn child. Meanwhile, Luke decides to change his situation in life and buy a new boat; Logan comes home drunk and reveals to Rory his failed business venture, and then runs off to Las Vegas with his buddies.
Lorelai, Rory and Emily take a road trip to North Carolina to attend a wedding; Lane goes into labor.
During Stars Hollow's annual Spring Fling festival, a huge hay bale maze leads to a chance encounter for Luke and Lorelai, where they apologize to one another and talk about the problems that led to their engagement being called off. As Rory shows Logan around town, Lorelai begins to feel that Logan might be too irresponsible for her daughter; meanwhile, Rory has a job interview with the Providence Journal Bulletin.
Lorelai heads to Luke's for her first breakfast there in a while – overall, it's an awkward experience for them both. Later on, when Lorelai's Jeep breaks down, Luke helps her shop for a new car. They argue and fight, which Lorelai thinks is ultimately a good sign. Paris considers breaking up with Doyle so she can be free of influences when it comes to picking which law or medical school she will attend. Rory receives a letter that will certainly influence her future plans.
Rory stresses out as graduation approaches, which leads to a day of eating and shopping with Lorelai. Later, with Luke in tow, the Gilmores hit the bars, where Lorelai takes the stage for a karaoke number obviously intended for Luke. Logan returns from a business trip and looks to discuss his and Rory's future with Lorelai.
Lorelai and Christopher are reunited at a party Emily and Richard throw in honor of Rory's graduation. Logan surprises everyone at the party by proposing to Rory, but she is too shocked to give him an answer. Then, on graduation day, Rory and Paris receive their diplomas, and Rory finally gives Logan her answer. Meanwhile, Lorelai is embarrassed about her recent karaoke serenade to Luke, and Luke is hurt when he overhears her saying it didn't mean anything.
Rory gets a job following the presidential campaign of one of the candidates running for president. While she prepares to leave in a mere three days, Lorelai adjusts to the idea that she may not see her daughter again for weeks, even months. Meanwhile, Luke is still trying to sort out how he really feels about Lorelai after they locked eyes at the karaoke jam. To see Rory off before she leaves for her new job, the entire town puts on a farewell party, despite the presence of rain.