Lorelai wakes up the morning after her night with Christopher. Though Christopher begs her to stay, Lorelai makes a quick exit and heads home. There, Lorelai starts to get rid of everything that reminds her of Luke and nearly empties her home of everything. Meanwhile, Rory gets a toy rocket ship as a gift from Logan and is confused by its meaning. She soon decides to go to London for the summer with him and soon learns that he already bought her a ticket so she can visit him for Christmas. Elsewhere, Kirk and Taylor cause an accident that seriously damages Luke's and Luke arrives a Lorelai's with a startling proposal.
When Logan has to cancel his trip to Asia with Rory, Lorelai tries to cheer up Rory by transforming her house into an Asia-themed get-away. Lane returns from her honeymoon with Zach, which didn't go as well as planned. Meanwhile, Luke tells T.J. about his breakup with Lorelai, leading T.J. and Liz to invite him over for dinner. Later, Lorelai and an obviously upset Luke run into each other in town and Rory is furious when she learns that Lorelai slept with Christopher.
Lorelai breaks the news of her break-up with Luke to Emily and Richard and has a startling realization about her emotional life when her parents have no reaction whatsoever. Later, Michel convinces Lorelai to attend a cotillion dance that Emily has planned and while there, Lorelai has a chance to reflect on her childhood, seeing that some things her parents made her do weren't all that bad. Meanwhile, Rory struggles to make her long-distance relationship with Logan work, and Christopher makes a confession to Lorelai after he has a dinner with Rory.
As Lorelai and Christopher begin to date, Lorelai finds it difficult to commit to the relationship wholeheartedly. Seeing this, Christopher plans romantic dates for Lorelai in order to win her heart. At Yale, Rory becomes friends with eccentric girls she meets at an art museum and Richard is a guest lecturer at his Alma mater. Meanwhile, April comes to Stars Hollow to stay with Luke for a few weeks while her mother is out of town and Lorelai has to bail Emily out of jail when she is arrested.
Lorelai brings Christopher to Friday night dinner, much to Richard and Emily's delight. However, when Christopher tells everyone that Sherry sent him a letter about how much she regrets leaving him and Gigi and how she wants Gigi to come visit her in Paris, Christopher and Lorelai get into an argument during dinner. Logan returns to the States on business and surprises Rory. At first Rory is ecstatic to see him, but after having dinner with Logan and his new business colleagues, she soon realizes that she's not a part of his business world. Meanwhile, Stars Hollow is covered in a bad odor when a train carrying pickles derails and Taylor refuses to pay for cleanup.
Christopher convinces Lorelai to accompany him to Parents' Day at Yale to visit Rory, and Lorelai is surprised to find that Emily and Richard are there as well. At Yale, Christopher tries prove himself as a 'cool dad' by inviting the Yale Daily News staff to an expensive lunch. However, all of Rory's co-workers drink too much, resulting in a bad situation when Rory gets wind of a breaking story and the staff has to leave. Meanwhile, Luke takes April to her swim team practice where the coach insists that Luke takes adult swim classes. During the lesson, the coach flirts with Luke and the two end up going on a date.
Christopher and Lorelai travel to Paris to take Gigi to visit Sherry and have a romantic and wonderful time together enjoying the sights of Paris as well as each other. Meanwhile back in Connecticut, Rory nears the end of her time as Editor-in-Chief of the Yale Daily News and begins to stress out when the reality of her uncertain future catches up to her. To cheer Rory up, Olivia and Lucy suggest that they travel to Stars Hollow for a girls' night while Lorelai is out of town. However, Rory gets a shock when she discovers that Lucy's boyfriend is Marty, who pretends that he doesn't know Rory. Later, Lorelai and Christopher return home with a surprise for everyone.
Lorelai has Rory over for dinner to tell her that she and her father got married while they were in Paris. While Christopher is in the room, Rory pretends that she's thrilled about the marriage, but later confesses to Lorelai how angry she actually is. With Logan back in town for the launch of his Internet company, he invites Rory to the launch party where a magazine editor encourages her to write about the event. However, Rory writes the article about the elite lives of the guests, hurting Logan and causing him to call her a hypocrite for living for free in his apartment, leading Rory to move out. Meanwhile, when April needs medical attention, Luke is forced to turn to Lorelai for help.
Lorelai starts to avoid Christopher during her daily life in Stars Hollow, leading her to admit to him that she's worried her friends and neighbors won't accept him. Upon hearing this, Christopher tries to bond with the people of Stars Hollow, but his efforts end up bringing the town knit-a-thon to an early end. Meanwhile, Olivia throws a 2002-themed party for Lucy, providing the perfect opportunity for Rory to confront Marty. Elsewhere, Luke learns that Anna is moving to New Mexico with April and demands equal rights to April from her.
Lorelai and Luke share a touching moment together when Luke brings by Liz's new baby for Lorelai to meet. When Christopher witnesses their moment, he begins to think that Lorelai isn't whole-heartedly in their marriage. Later, Christopher and Luke have an angry confrontation after Lorelai and Christopher argue over exchanging vows at a party Emily is throwing and Luke is forced to hire a lawyer due to custody issues with Anna. Meanwhile, Logan reveals to Lucy that Marty and Rory are acting like they've met recently and Emily warns Lorelai about her marriage.
After spending her holiday break in London, Rory returns to the states. Lorelai, disappointed that she didn't get to spend Christmas with Rory, decides to throw a Christmas after Christmas' celebration as a family with the works -- a big, decorated tree, decorations, and shopping. Meanwhile, Luke asks Lorelai to write him a letter of recommendation to aid him in his custody battle with Anna over April.
Lorelai confronts Jackson after she notices that Sookie's behavior has been off recently. Luke and Anna square off at a custody hearing regarding April. At Yale, with Paris' help, Rory is able to get Lucy, who recently broke up with Marty, to forgive her. Later at Yale, Rory attends one of Richard's lectures and is shocked by what she sees. Elsewhere, Christopher finds the character letter that Lorelai wrote for Luke and confronts Lorelai about their relationship.
Richard is admitted to the hospital and Lorelai, Rory and Emily nervously wait for news on his condition. Logan hears about what's happened and borrows a helicopter in order to be there for Rory. Lorelai, however, cannot reach Christopher, who is still angry over their fight, to tell him the news. Lorelai, upset that Emily is focused on her social calendar in order to stay calm, is relieved when Luke arrives unannounced and runs errands for Emily. When Christopher finally arrives, the scene at the hospital is more than he can handle.
Days after his bypass, Richard begins the slow road to recovery and the Gilmores attempt to return to normalcy. Rory goes back to Yale and finds that her grandfather's class is now being taught by a young, attractive professor who catches Rory off-guard with his charm. In Stars Hollow, Lorelai tries to forget about her marital problems by helping Sookie plan a funeral for one of Michel's beloved dogs. Later, Christopher returns home and confronts Lorelai about the main issue hurting their marriage -- Lorelai's feelings for Luke.
At Friday night dinner, Lorelai finally decides to tell her parents that her marriage to Christopher has fallen apart, but doesn't get a chance to when an argument breaks out over Emily's new healthy, no-alcohol meals to help Richard recover from his heart attack. Lorelai gets Sookie to cook healthy and tasteful meals for Richard and Lorelai helps Emily with Richard's various business affairs. While helping her mother, Lorelai finally admits to Emily that her marriage to Christopher is over. Meanwhile, Rory attends Logan's birthday dinner and has an awkward encounter with Mitchum who asks Rory to keep Logan on track. Logan later receives disturbing news about an online company he recently purchased. Elsewhere, T.J., Liz, and the baby stay with Luke while their house is fumigated.
While planning a baby shower for Lane, Rory gets an unexpected call from the The New York Times offering her an interview. Rory scrambles to prepare for the interview leaving Lorelai to take over baby shower preparations. As Lorelai plans, she finds her self running interference between Lane and Mrs. Kim as they bicker over how Lane will raise the twins. Logan admits to Rory that his business venture went bad, and Rory offers him full support until Logan begins to revert back to his old ways by traveling to Las Vegas with Colin and Finn to blow off steam. Meanwhile, when Luke finds that Liz and T.J. are trying to sell his boat, he decides to make big changes in his life by taking April on a boat trip for the summer. Lastly, Lane is placed on bed rest and has to be wheeled in her bed across town to her party at Miss Patty's.
Lorelai takes a road trip to North Carolina to attend Mia's wedding, and after Rory has a fight with Logan over his immaturity, she agrees to go with. Emily invites herself on the road trip to get away from Richard, who is driving her crazy as he continues to recover from his heart attack. At the wedding, Emily becomes upset by how close Mia is with Lorelai and Rory. Later, Lorelai learns that Emily came to the inn several years ago to ask Mia for pictures of Lorelai and Rory from the years they weren't speaking. Logan makes a surprise visit to the wedding to get Rory to forgive him. Meanwhile, Lane and Zach ask Luke to be the godfather to their twins. Finally, when Lane goes into labor, Luke helps get everyone to the hospital.
As the citizens of Stars Hollow prepare for the annual Spring Fling festival, Rory decides to bring Logan home with her and takes him around the town. Lorelai, seeing how close the two have become, begins to worry that Logan's immaturity and irresponsibility make him someone that Rory shouldn't be with. Meanwhile, Taylor upsets the town when he blows the entire Spring Fling budget on a large hale bale maze. In the maze, Lorelai and Luke run into each other and there they admit that they each made mistakes that ultimately lead to the ending of their engagement as well as apologize for their actions. Lastly, Rory heads to an interview with the Providence Journal-Bulletin, but has a hard time making decisions that will affect not only her career, but the rest of her life.
Lorelai goes to Luke's for breakfast for the first time since their engagement break-up, but they both soon find that it's awkward to be around each other after everything that has happened. Later, when Lorelai's Jeep dies, she has Luke help her shop for a new car. While at the dealership, Lorelai and Luke's tension between one another mounts into a huge fight, which Lorelai takes as a good sign. Meanwhile, Paris, who has been accepted to dozens of law schools and medical schools, decides she has to break up with Doyle so their relationship doesn't play a part in her decision as to which post-graduate program to attend. Finally, Rory receives a letter that will change her future plans.
With graduation rapidly approaching, Rory begins to become more and more stressed about her future. Lorelai tries to cheer her up by planning the perfect day of shopping and eating. Later, after seeing that Luke is once again wearing the blue baseball cap, Lorelai invites him to come with her and Rory to karaoke night at a nearby bar. After drinks, Lorelai sings an emotion-filled song, noticeably directed toward Luke. Meanwhile, Logan returns to Connecticut after a business trip in California and pays a visit to Lorelai to discuss his future plans with Rory.
The day before Rory's graduation from Yale, Emily and Richard throw Rory a party and during which they perform a song in her honor. During the party, Lorelai and Christopher come face-to-face for the first time following their separation and thrilled to find that they can still be friends despite their recent rocky relationship. Logan makes a shocking move at the party when he asks Rory to marry him, but Rory, stunned and unable to give him an answer, turns to Lorelai to help her make a decision. Later, Rory and Paris graduate from Yale and Rory gives Logan an answer. Meanwhile, Lorelai and Luke's relationship takes a step back when Luke overhears Lorelai saying that the karaoke serenade meant nothing.
As Rory rejoices after landing her dream job, Luke gets the residents of Stars Hollow together to throw Rory a grand graduation party. Emily and Richard are in attendance and listen teary-eyed with the rest of the guests as Rory gives a speech thanking Lorelai and everyone else for their support. Luke's thoughtfulness and kind gestures for Rory result in an unexpected reaction from Lorelai. Later, the morning that Rory leaves Stars Hollow, Luke opens the diner early for one last Gilmore girls diner breakfast before Rory heads out into the world as a political journalist.