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Rory meets her idol CNN journalist Christiane Amanpour at the Inn. Although Lorelai and Rory have planned a crazy roller coaster tour for the summer, they must postpone their trip when a wonderful opportunity comes to Rory. Luke enlists the help of everyone in Stars Hollow to throw Rory a surprise bon voyage party. Lorelai is staying maniacally busy trying to cope with Rory's impending departure. When Babette's swollen ankles alert her to an approaching rainstorm, Luke stays up all night preparing for the downpour. His thoughtfulness brings an unexpected reaction from Lorelai.
On the eve of Rory's graduation, Emily and Richard throw her a party. At the party, Lorelai and Christopher are reunited for the first time since their separation, and both are relieved to find they can still be friends.
Logan surprises everyone at the party with a very special graduation gift for Rory.
On graduation day, Rory and Paris receive their diplomas. Meanwhile, Lorelai is embarrassed about her karaoke serenade to Luke the night before.
With graduation looming, Rory is anxiety-ridden over her future, so Lorelai tries to cheer her up with a day of eating and shopping. Lorelai notices happily that Luke is once again wearing the baseball cap she gave him, and invites him to join her and Rory for karaoke night at a local bar. After a few drinks, Lorelai takes the stage to sing a heartfelt number which is obviously directed at Luke. Logan returns from a business trip to California and comes to see Lorelai to discuss his future with Rory.
Lorelai stops into Luke's diner for breakfast for the first time since their break-up, but finds they are awkward and uncomfortable together. Later, Lorelai's Jeep breaks down and she asks Luke to help her shop for a new car. While they look at cars, Lorelai and Luke's irritation with one another finally explodes into a fight, which Lorelai secretly takes as a good sign. Meanwhile, Paris gets accepted to numerous law schools and medical schools, and decides she must break up with Doyle so their relationship won't influence her choice of a graduate school. Finally, Rory gets a surprising letter that will have an impact on her future plans.
As Stars Hollow prepares for its annual Spring Fling festival, Rory brings Logan home and shows him around town. Lorelai sees how serious their relationship has become and worries that Logan is too irresponsible for Rory. Taylor angers the town by spending the entire Spring Fling budget on a huge hay bale maze. At an unexpected encounter in the maze, Lorelai and Luke apologize to one another and admit they both made mistakes that led to the end of their engagement. Meanwhile, Rory has a job interview with the Providence Journal Bulletin and struggles with decisions about her future.
Lorelai plans a road trip to North Carolina to attend the wedding of Mia, the woman who took in Lorelai and Rory and served as a surrogate mother/grandmother for many years. Rory has a fight with Logan over his immature reaction to his business disaster, and agrees to go on the trip with Lorelai. Emily invites herself along in an effort to get away from Richard, who is driving her crazy while he recuperates at home. At the wedding, Emily is upset by the close relationship Mia shares with Lorelai and Rory. Lorelai learns that Emily came to see Mia five years earlier to ask for pictures of Lorelai and Rory during the years they were estranged. Logan makes a surprise appearance and asks Rory to forgive him. Meanwhile, Lane and Zach ask Luke to be the godfather to their twins. Finally, Lane goes into labor and Luke helps get everyone to the hospital.
While planning Lane's baby shower, Rory gets a call from The New York Times offering her an interview for the Reston Fellowship. Lorelai finds herself brokering peace between Lane and Mrs. Kim over how the twins should be raised. Logan finally admits his business disaster to Rory. When Luke discovers that Liz and T.J. are trying to sell his boat, he decides to make some changes in his life. Lane is put on bed-rest
At Friday night dinner, Lorelai works up the courage to tell her parents about the break-up of her marriage, but is derailed by their argument over the healthy meals and no-alcohol policy Emily has instituted to help Richard recover from his heart attack. Lorelai enlists Sookie to bring Richard healthy but delicious meals, then helps Emily organize Richard's business affairs. Over a shared bottle of scotch, Lorelai finally tells her mother about the breakup of her marriage. Rory attends an awkward birthday dinner for Logan with Mitchum Huntzberger, who asks her to help him 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.
Two days after his by-pass surgery, Richard is on the road to recovery, and Rory returns to Yale, where she finds that Richard's economics class is now being taught by an attractive young TA, Tucker Culbertson, who flusters Rory with his charm.
While Lorelai tries to distract herself from the issues in her marriage, she and Sookie focus on planning a funeral for one of Michel's beloved dogs. Finally, Christopher returns ready to talk, and he and Lorelai discuss the main problem that has haunted their marriage – Lorelai's feelings for Luke.
In the 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 the night before. Upset by Emily’s attempt to remain calm by dealing with her social calendar, Lorelai is relieved when Luke shows up unannounced 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 when he sees Lorelai talking to Luke.
Lorelai notices some odd behavior from Sookie. Luke and Anna attend a custody hearing. With help from Paris, Rory finally makes amends with Lucy. While attending Richard's economics class at Yale, Rory witnesses a frightening scene. Christopher finds the letter Lorelai wrote for Luke and confronts her.
Lorelai postpones Christmas celebrations until Rory returns from London. Luke asks Lorelai to write a character recommendation for his custody battle over April. Lorelai struggles with the task. Rory decides she will write an apology letter to her friend Lucy.
Luke and Lorelai share a sweet moment when Luke introduces her to Liz's new baby. Christopher begins to question Lorelai's commitment to their marriage. Lorelai and Christopher fight over the elaborate wedding party Emily is planning. Luke contacts a lawyer over his custody troubles with Anna. Christopher and Luke have an ugly confrontation. Logan discovers that Rory and Marty have been hiding their real relationship from Lucy. Finally, Emily gives Lorelai a unsolicited marriage advice.
When Christopher questions Lorelai about why she has avoided involving him in the daily life of Stars Hollow, she admits her concern that her old friends may not accept him. Christopher makes an effort to bond with the townspeople, and Lorelai brings him to the town knit-a-thon, where his well-intentioned gesture brings the event to an early end. When Olivia throws a 2002-themed birthday party for Lucy, Rory gets her chance to confront Marty about his coldness toward her. Finally, 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.
Lorelai invites Rory over to dinner to tell her that she and Christopher got married in Paris. Rory pretends to be thrilled while Christopher is in the room, but later tells Lorelai how hurt and angry she really is. Logan surprises Rory with a visit and an announcement that he is relocating to New York to start his new internet company. Meanwhile, when April faces a medical emergency, a frantic Luke turns to Lorelai for help.
Christopher and Lorelai take Gigi to visit her mother in Paris. They have a wonderful, romantic time enjoying the city. 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 and her new friends, Olivia and Lucy, help her cope. Rory finally meets Lucy's new boyfriend. Christopher and Lorelai return home with a surprise for everyone.
Christopher and Lorelai visit Rory during Parents' Weekend at Yale. Christopher invites Rory's co-workers on the Yale Daily News to a lunch where they all drink too much. The meal ends abruptly when they must leave to cover a breaking story. Meanwhile, Luke meets April's swimming coach with interesting results.
Emily and Richard are delighted to see Lorelai and Christopher are dating. Sherry has contacted Christopher regarding visitation with Gigi. Logan returns to town for a surprise visit. Rory is thrilled until she meets her colleagues. Meanwhile, Stars Hollow is plagued by a terrible odor.
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 Anna is out of town. Finally, Emily gets arrested and Lorelai has to bail her out of jail.
When Richard and Emily have no real reaction to the news of her break up with Luke, 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 beautiful cotillion dance, Lorelai discovers that some things her parents wanted for her weren’t really that terrible. Rory has a tough time making her long-distance relationship with Logan work. After taking Rory out for a father/daughter dinner, Christopher makes a startling confession to Lorelai.
Rory is upset over Logan's absence and the fact that they had to cancel their 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. Lane returns from her disastrous honeymoon. While repairing the damage to the diner, Luke tells TJ about his break-up with Lorelai, prompting TJ and Liz to invite Luke for dinner. When Luke and Lorelai run into each other in town, Luke can't hide his anger over their breakup. Finally, Rory is furious when she learns that Lorelai slept with Christopher.
Picking up on the day after last season's finale, Lorelai wakes up in bed with Christopher. Once at home, Lorelai tries to get rid of everything that reminds her of Luke. Rory receives a strange good bye gift from Logan. She decides she should join him in London for the summer, only to learn Logan has other plans. Kirk and Taylor cause a bizarre accident that damages Luke's diner. Finally, Luke shows up at Lorelai's door and asks her to elope.
