Lorelai and Luke begin to plan out their future as husband and wife, but Luke is soon mortified when word gets out that Lorelai was the one who popped the question.
Lorelai takes in a dog to keep herself from being too lonely. She and Luke try to figure out whether or not to buy the Twickham home or just remodel hers. Meanwhile, Rory begins her community service hours, but when she visits Luke at the dinner and finds out that he and Lorelai are engaged, she begins to feel estranged from everybody.
Lorelai tries not to give into the pressure to pick a wedding date by Sookie. Rory gets a job at the Daughters of the American Revolution with Emily, but Emily uses her to pick out her competition for its presidential election.
Sookie tries to get Lorelai and Rory on speaking terms again by making them godmothers of her two kids. Lorelai gets upset, though, when she learns that Rory didn’t share her new cell phone number with her. Meanwhile, Logan tries to coax Rory into taking a madcap dash with him into New York.
Rory manages to put together a great gala for the Daughters of the American Revolution, but during the event, Richard has words with Logan’s father Mitchum about his critical approach to Rory’s writing, while Emily confronts Logan’s mother about her son’s fast-paced courtship of Rory.
Logan is surprised when Richard turns to him for insights into Rory’s next moves, but assumes he is really being asked about whether or not the couple intends to wed.
Lorelai and Rory each lament the fact that not being on speaking terms will keep the pair from celebrating Rory’s 21st birthday in their own special way. Lorelai also balks at Richard’s request that she help him convince Rory to go back to school. Meanwhile, Emily, who decides to go all out on a birthday celebration for Rory, learns, along with Richard, that Rory and Logan are in a sexual relationship.
Rory is happy to see Jess return to Stars Hollow with good news about what his life has been like in recent times, but when she decides to go to dinner with both him and Logan, an argument erupts, prompting her to rethink her own life's recent path.
Lorelai receives a phone call from Christopher which could have dire consequences for her and Luke, while Luke is shaken by an unexpected visitor from his own past. Meanwhile, Rory and Lorelai try to reach out to one another, as Rory readies to look towards a brighter future.
Christopher tries to reinsert himself into Rory and Lorelai's lives, but Luke has trouble accepting his newfound presence. Lorelai is pleased to have Rory for her first Thanksgiving at the Dragonfly Inn, but Rory is troubled by some news about Logan. Meanwhile, Lane has trouble sorting out the jealous egos of bandmates Brian and Zach.
After learning he had a daughter he never knew about, Luke tries to reach out to the girl's mother, Anna. Lorelai has premonitions of doom as she picks out her wedding dress and sets a date. Meanwhile, Rory, Paris and Doyle find an off-campus apartment together near Yale, but, despite her conflict with Logan, Rory soon finds herself touched by Logan's sudden appearance on her doorstep.
As the winter carnival approaches, Luke continues to struggle with telling Lorelai about his 12-year-old daughter, April, but April's desire to spend more time with him at work could complicate the situation.
Lorelai tries to roll with the new family dynamic that having April in her and Scott's life will bring. Rory becomes fed up when Paris' lack of leadership ability at the Yale Daily News causes the entire staff to resign, prompting her to utilize Logan's assistance to finish the latest issue of the paper for its deadline.
Emily and Richard have Luke over for one of their dinners with Lorelai, during which Lorelai keeps the news of their delayed wedding to herself, but the night soon turns into an interrogation of Luke.
Rory and Logan bring Lorelai and Luke with them to Logan's family's Martha's Vineyard retreat during Valentine's Day, but Luke's disdain for Logan rears its head again. Logan and Luke end up bonding, however, when Logan comes to Luke's aid on a Valentine's Day gift for Lorelai. Meanwhile, Logan's dad turns up at the house fuming mad and puts an abrupt end to the weekend fun.
Lorelai and Christopher go up to Yale to watch Rory in a journalism debate, after which Lorelai then agrees to babysit Christopher's daughter, G G, for an afternoon.
After forgiving Logan for his one-night stands during their time apart, Rory decides to go home to spend some time with Lorelai, who is upset that Luke is taking a trip alone with April. Rory then decides to do some snooping on April to learn more about her. Meanwhile, Zack is shocked by the reaction of Lane's mother to his request to marry Lane.
Lorelai has a dream that involves the crooner Paul Anka. Logan heads out with his daredevil friends for some rowdy fun after he is unable to get past the idea that though he is back with Rory, she does still not fully trust his fidelity.
Lorelai and Rory try to throw Lane a bachelorette party with disastrous results, but as Zach's bachelor party ends in a similar fate, the two sides end up partying together. Meanwhile, Lorelai is informed by Mrs. Kim that without a date, she can't come to the wedding, as Luke is still out of town, but she rings up Christopher to fill in.
Luke throws April a birthday party for all her friends at the diner, but upsets Lorelai when he tells her it may not be the right time for her to be introduced to April.
Emily gets Lorelai to serve as her eyes after undergoing a minor eye procedure and ends up opening up to her in an unexpected way. Logan is discharged from the hospital and Rory takes it upon herself to tend to him. Meanwhile, Luke tries to assist Liz and TJ with their as-yet unborn child.
When the town troubadour is discovered, troubadours from all over flock to Stars Hollow to get themselves heard as well. Rory organizes a party for Logan on the eve of his graduation, which is also the night before his departure for London, but laments the distance that will come between them.