Instead of celebrating Christmas while Rory was in London, Lorelai and Christopher put their holidays on hold. Once Rory returns to Stars Hollow, they decorate several Christmas trees, do their shopping and even bake Christmas cookies for the first time as a family. After showing up unexpectedly at the inn, Luke asks Lorelai to write a character recommendation letter to help in his custody battle over April. Lorelai struggles to write the letter, until she and Rory run into Luke and April at the mall, and Lorelai suddenly remembers how important Luke has always been in Rory’s life. Meanwhile, Rory decides to write an apology letter to her friend Lucy, explaining why she and Marty kept their past friendship a secret.
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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.
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 distract herself from her own sad love life, Lorelai turns her house into an Asian-themed wonderland. Lane returns from her disastrous honeymoon. While repairing the damage to the diner, Luke tells his brother-in-law, T.J., about his breakup with Lorelai, prompting T.J. and Luke's sister, Liz, to insist that Luke come over for dinner and sympathy. When Luke and Lorelai run into each other in town, Luke can't hide his anger over their breakup. And Rory is furious when she learns that Lorelai slept with Christopher.
When Richard and Emily display no real reaction to the news of her breakup with Luke, Lorelai 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 beautiful 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 with Logan work. And after taking Rory out for a father/daughter dinner, Christopher makes a startling confession to Lorelai.
Lorelai and Christopher have resumed their relationship, and although Lorelai is finding it difficult to fully commit to him, Christopher keeps coming up with romantic dates to win her over. Meanwhile, at Yale, Rory meets some eccentric new girlfriends at an art exhibit, and Richard becomes a guest lecturer. Also, April comes to stay with Luke for a few weeks while her mother, Ana, is out of town. And when Emily gets arrested, Lorelai must bail her out of jail.
Emily and Richard are delighted when Lorelai and Christopher attend Friday night dinner together as a couple. After Christopher reveals that his ex-wife, who lives in Paris, wants him to send their daughter, G.G., there for a visit, Lorelai argues with him over dinner. Meanwhile, in town on business to acquire an Internet company, Logan visits the surprised Rory. Although she is thrilled, Rory realizes during a dinner with Logan's colleagues that she has no connection to his new business world--and she is especially threatened by one of his beautiful co-workers. Also, Stars Hollow is plagued by a terrible odor when a train with a full load of pickles derails, and Taylor refuses to pay for the cleanup.
After Christopher persuades Lorelai to visit Rory at Yale during Parents' Weekend, Lorelai is surprised to find that Richard and Emily are also there. Trying to impress Rory's co-workers at the Yale Daily News, Christopher invites them to an expensive lunch, where they all drink too much. The meal ends abruptly when Rory insists that everyone has to leave and 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, G.G., to visit G.G.'s mother in Paris. Despite severe jet lag, Christopher and Lorelai manage to have a wonderful, romantic time enjoying the city and each other. Back in Connecticut, 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 while Lorelai is out of town. Upon returning, Rory is surprised to find that Lucy's new boyfriend is Rory's old friend Marty, who pretends not to know Rory. And later, Christopher and Lorelai return home with a surprise for everyone.
After Lorelai invites Rory to dinner and tells her that she and Christopher got married in Paris, Rory pretends to be thrilled while Christopher is in the room. But she later tells Lorelai how hurt and angry she really is. Meanwhile, back in town for the startup of his new Internet company, Logan invites Rory to the launch party, where she meets a magazine editor who suggests that she write an article on the event. But when Rory writes a judgmental article, describing the guests as spoiled elitists, Logan accuses Rory of hypocrisy, considering she is living rent-free in his apartment. Defensive at first, Rory eventually realizes that she is living a double standard and decides to find her own apartment. Meanwhile, when April faces a medical emergency, Luke frantically turns to Lorelai for help.
When Christopher asks Lorelai why she has avoided involving him in the daily life of Stars Hollow, she admits that she is concerned her old friends will not accept him. In an effort to help him bond with the townspeople, Lorelai brings Christopher to the town knit-a-thon, where his well-intentioned gesture brings the event to an early end. Meanwhile, when Olivia hosts a 2002-themed birthday party for Lucy, Rory gets a chance to confront Marty about his coldness toward her. Also, Luke is touched by the birth of Liz and T.J.'s baby, and when he learns that Anna is planning to move to New Mexico with April, he demands equal rights as a parent of April.
While introducing Lorelai to his sister's new baby, Luke shares a sweet moment with her. But when Christopher witnesses the scene, he becomes concerned that Lorelai isn't fully committed to their marriage. Later, the two fight over whether or not they should exchange vows at the elaborate wedding party that Emily is hosting for them. And Luke and Christopher have an ugly confrontation on the streets of Stars Hollow. Meanwhile, upon discovering that Rory and Marty have been pretending that they just met, rather than admitting their previous friendship to Rory's friend Lucy, Logan reveals the truth to her. Also, Emily gives Lorelai a warning about her marriage. And Luke contacts a lawyer over his custody troubles with Anna.
Instead of celebrating Christmas while Rory was in London, Lorelai and Christopher put their holidays on hold. Once Rory returns to Stars Hollow, they decorate several Christmas trees, do their shopping and even bake Christmas cookies for the first time as a family. After showing up unexpectedly at the inn, Luke asks Lorelai to write a character recommendation letter to help in his custody battle over April. Lorelai struggles to write the letter, until she and Rory run into Luke and April at the mall, and Lorelai suddenly remembers how important Luke has always been in Rory's life. Meanwhile, Rory decides to write an apology letter to her friend Lucy, explaining why she and Marty kept their past friendship a secret.
After noticing Sookie's recent odd behavior, Lorelai forces Jackson to tell her the reason for it. Meanwhile, 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. And Christopher finds the character reference that Lorelai wrote for Luke and confronts her.
In a hospital waiting room, Lorelai, Rory and Emily anxiously await word on Richard's condition. When Logan hears what is happening, he borrows a helicopter to be by Rory's side, but Lorelai is unable to reach Christopher, who is still angry over their fight from the night before. Upset because Emily is attempting to remain calm by dealing with her social calendar, Lorelai is relieved when Luke shows up unexpectedly and volunteers to run errands for Emily. Christopher finally arrives to be with Lorelai, but the scene at the hospital is more than he can take.
Two days after his heart bypass surgery, Richard is on the road to recovery. When Rory returns to Yale, she finds that Richard's economics class is now being taught by an attractive young professor, Tucker Culbertson, who flusters Rory with his charm. Meanwhile, trying to distract herself from the issues in her marriage, Lorelai joins Sookie in focusing on the funeral of one of Michel's beloved dogs. After Christopher returns ready to talk, he and Lorelai discuss the main problem that has haunted their marriage: Lorelai's feelings for Luke.
At a Friday night dinner, Lorelai prepares to tell her parents about the end of her marriage, but she is derailed by their argument over the policy of healthy meals and no alcohol that Emily has instituted to help Richard recover from his heart attack. Lorelai enlists Sookie to bring healthy and delicious meals to Richard and then helps Emily organize Richard's business affairs. Over a shared bottle of scotch, Lorelai finally tells her mother about the breakup. Meanwhile, Rory attends an awkward birthday dinner for Logan with his father, Mitchum, who asks her to help steer Logan in the right direction. Later, Logan receives disturbing news about the online company he purchased. Also, Luke shares his home with Liz, T.J. and their baby daughter while their house is being fumigated.
In the midst of planning Lane's baby shower, Rory receives a long-awaited call from The New York Times offering her an informational interview. Lorelai takes over the shower-planning duties and finds herself brokering peace between Lane and Mrs. Kim over how Lane plans to raise her twins. Meanwhile, Logan finally admits his business disaster to Rory, who offers him her full support. But when Logan announces that he is flying to Las Vegas to blow off steam with his old college pals, Rory is disappointed and worried. After Luke discovers that Liz and T.J. are trying to sell his boat, he decides to make some changes in his life and take April on a long boat trip over the summer. And Lane is ordered to rest, resulting in her being wheeled through Stars Hollow in her bed to attend the shower at Miss Patty's place.
Lorelai and Rory plan a road trip to North Carolina to attend the wedding of Mia, a woman who served as their surrogate mother/grandmother for many years. Emily invites herself on the trip in an effort to get away from Richard, who is driving her crazy while he recuperates at home. At the wedding, Emily becomes upset by the close relationship Mia shares with Lorelai and Rory. Lorelai learns that Emily had visited Mia during the years they were estranged to ask for pictures of Lorelai and Rory. And Logan makes a surprise appearance to ask Rory to forgive him for his immature reaction to his business disaster. Meanwhile, Lane and Zack ask Luke to be the godfather of their twins. When Lane goes into labor, Luke helps everyone get to the hospital.
As Stars Hollow prepares for its annual Spring Fling festival, Rory brings Logan to her hometown and shows him around. When Lorelai sees how serious the relationship has become, she worries that Logan is too irresponsible for Rory. Meanwhile, Taylor angers the town by spending the entire Spring Fling budget on a huge hay bale maze. During an unexpected encounter in the maze, Lorelai and Luke apologize to each other and admit they both made mistakes that led to the end of their engagement. Also, Rory gets a job interview with the Providence Journal-Bulletin and struggles with decisions about her future.
When Lorelai visits Luke's diner for the first time since their breakup, she finds that they are awkward and uncomfortable together. Later, Lorelai's Jeep breaks down, and she asks Luke to help her shop for a new car. But Lorelai and Luke's irritation with each other finally explodes into a fight--which Lorelai secretly takes as a good sign. Meanwhile, after Paris is accepted into numerous law schools and medical schools, she decides she must break up with her boyfriend so their relationship won't influence her choice of graduate school. And Rory gets a surprising letter that impacts her future plans.
As her final examinations approach, Rory has a scary dream about her future. Richard and Emily announce that they are going to buy a pied-à-terre in New York City--but Rory has some news that might change their plans. Later, Lorelai rocks a karaoke bar with a serenade to Luke.
On the eve of Rory's graduation, Emily and Richard host a party and perform a song in her honor. At the fete, Lorelai and Christopher reunite for the first time since their separation, and both are relieved to find that they can still be friends. Logan surprises everyone by proposing marriage to Rory--but she is too shocked to give him an answer and begs Lorelai to help her decide what to do. 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 he is hurt when he overhears her saying it didn't mean anything.
In the emotional series finale, after Rory lands her dream job as a political reporter, Luke enlists the help of everyone in Stars Hollow to throw her a graduation party. Emily and Richard attend the huge gathering, at which Rory makes a speech thanking Lorelai and the whole town for giving her such a great start in life. Luke's thoughtfulness brings out an unexpected reaction from Lorelai. Finally, on the morning that Rory leaves Stars Hollow to start her career, Luke opens the diner before dawn to share a celebratory breakfast with the Gilmore girls. CNN journalist Christiane Amanpour makes a cameo appearance as a guest at the Dragonfly Inn.