Picking up on the same night as last season's finale, Lorelai and Luke begin making plans for their future, but Luke is embarrassed when word spreads that Lorelai was the one who proposed. Still hurt over Rory's decision to drop out of Yale and move in with Emily and Richard, Lorelai tells her parents that they can take care of Rory from now on. Richard hires an old friend and respected attorney to help Rory get an easy sentence for stealing the yacht, but the judge gives Rory 300 hours of community service. Logan throws Rory a 'felon' party.
Rory begins serving her 300 hours of community service and finds that life on a road crew is not pretty. Lorelai and Luke try to decide whether they will fix up Lorelai's house or buy the Twickham house. Luke's sister Liz begs him to hire her husband T.J. as a contractor. When Rory pays Luke a surprise visit at the diner to find out how Lorelai is, he feels obligated to tell her that he and Lorelai are engaged. Afterwards, Luke confronts Lorelai about her estrangement from Rory. Feeling lonely, Lorelai adopts a dog at the Stars Hollow pet fair. Finally, during a chance meeting, Lorelai and Rory have an angry confrontation about their mutual hurt feelings.
Excited about catering the wedding, Sookie pressures Lorelai to set a date, but Lorelai won't commit. While completing her community service hours, Rory takes a job at Emily's DAR (Daughters of the American Revolution) office. Convinced that she has a rival for the job of DAR president, Emily uses Rory as her spy. Logan returns from Europe and returns to Yale, forcing Rory to confront her true feelings about dropping out of college. Lane and her band return from their summer on the road. Luke agrees to take care of Lorelai's dog, Paul Anka, while she works late at the inn, and ends up rushing the dog to the vet. Finally, Lorelai admits to Luke her reason for putting off their wedding.
Missing Rory, Lorelai tries to call her and is upset to find that Rory's cell phone is no longer in service. Sookie asks Lorelai and Rory to be the godparents to her two children in the hope that they will reconcile when they see each other at the ceremony. However, mother and daughter end up fighting when Lorelai realizes that Rory have her new cell number to Sookie but not to her. Logan learns that his father expects him to graduate this year and enter the family business. Wanting to break free from family pressures, Logan whisks Rory off to a weekend in New York.
Rory does a fabulous job organizing a big DAR bash for Emily. However, at the party, Richard confronts Logan's father, Mitchum Huntzberger, about his opinion of Rory's journalistic talents, while Emily has an even uglier confrontation with Logan's mother, Shria, over the romance between Rory and Logan. Meanwhile, after a small kitchen fire at the Dragonfly Inn, Lorelai needs Richard's help settling the insurance claim and uses the time spent with her father to needle him about the fact that he has been unable to get Rory to return to Yale. Though he's annoyed with Lorelai, Richard has to admit that Rory is not where she should be.
Richard tries to get information from Logan about Rory's future plans, but Logan mistakenly thinks that Richard is asking when the two of them plan to marry. Lorelai is in favor of Taylor's plan to change all the Stars Hollow street names back to their original historic names, until she learns that the street where the Dragonfly Inn is located was once known by a disgusting name. Rory makes a surprising confession to Logan. Richard finally faces the fact that he should never have let Rory drop out of Yale, and shows up at Lorelai's house to talk things over.
As Rory's twenty-first birthday approaches, both Lorelai and Rory are saddened by the fact that their ongoing estrangement will keep them from spending the day the way they had always planned. Richard tries to convince Lorelai to help him with a plan to get Rory back to Yale, but Lorelai insists that Rory has to make the decision herself. While Richard continues to worry about Rory's future, Emily throws herself into planning an elaborate birthday party. Meanwhile, Emily and Richard are shocked when they realize that Rory and Logan have been having sex.
Rory is pleasantly surprised when her old flame Jess appears at her grandparents' house and reveals an amazing development in his life. Rory agrees to go to dinner with Jess, and when Logan unexpectedly joins them, an ugly confrontation develops, leaving both Rory and Logan to face the choices they have made. Emily is concerned about Rory's sudden evasiveness and tries to exert some parental discipline. Meanwhile, Luke agrees to sponsor a local girls' soccer team and Lorelai channels all her concerns about Rory into caring for her dog, Paul Anka.
A surprise phone call from Christopher brings up issues of trust between Lorelai and Luke. Later, when a person from Luke's past shows up in Stars Hollow, he has no idea how to tell Lorelai about it. After months of estrangement, Lorelai and Rory make their first move toward reconciliation and Rory takes major steps to change the direction of her life.
After a long absence, Christopher reappears in Lorelai and Rory's lives with an offer to make up for lost time. Luke struggles with what the new person in his life will mean to him and his relationship with Lorelai. Lorelai and Rory enjoy their first Thanksgiving at the Dragonfly Inn, during which Rory receives surprising news about Logan. Meanwhile, as the band prepares for an important showcase performance, Lane has to deal with Zach's jealousy over a song Brian wrote about her.
Feeling that he has missed too much and wants to get to know his newly discovered daughter April, Luke goes to have a talk with her mother, his former girlfriend Anna Nardini. Meanwhile, Lorelai sets a date for the wedding after finding the perfect dress, but she is worried by the nagging feeling that something is about to go wrong. Back at Yale, Rory happily moves into a dingy off-campus apartment with Paris and Doyle, and tries to avoid running into Logan. However, when Logan shows up at her apartment and declares his love for her, Rory breaks down.
After not being able to work up the courage to tell Lorelai about his daughter, April throws Luke into a panic when she asks if she can spend the day at his diner. Much to Luke's horror, April and Lorelai begin talking at the diner and April mentions that Luke is her father. But Lorelai tries to support their relationship and offers to postpone the wedding so Luke and April can get to know each other better. However, Luke's reaction to her proposal leaves Lorelai hurt and confused. At Yale, Logan goes to great extents in an attempt to win back Rory's affection and the newspaper staff rebels against Paris at the Yale Daily News. Meanwhile, Rory, Lorelai, and Paul Anka run a fortune telling booth at the annual Winter Carnival and Zack gets jealous after seeing Lane with another guy.
With April now being a part his life, Luke has to cope with the significant changes her being there has caused. Lorelai also must deal with the changes that April has brought to her engagement to Luke and tries to convince herself, and everyone else, that she doesn't mind. At the Yale Daily News, Rory has to deal with the impact of the staff quitting in protest of Paris' management and enlists Logan's help to get the paper out on time. Meanwhile, Lorelai lets Richard and Emily know that they no longer will have to pay for Yale, resulting in a poignant Friday night dinner.
Emily, wanting to get to know her future son-in-law better, asks Lorelai to invite Luke over for dinner. However, Lorelai doesn't tell Emily about the postponement. Meanwhile, The Yale Daily News staff fires Paris and Rory takes over as editor. This angers Paris and she kicks Rory out of her apartment, leaving Rory to have to move in with Logan.
For Valentine's Day, Lorelai and Luke are invited to go to Martha's Vineyard with Rory and Logan. The trip is disrupted by Luke's constant bad attitude towards Logan, but his attitude soon changes when Logan helps him find a Valentine's Day gift for Lorelai. Once things begin to go better, Mitchum Huntzberger arrives, resulting in an ugly confrontation. Meanwhile, Luke has to put Lorelai's worries that they will never get married to rest.
Rory and Logan attend his sister, Honor's wedding. Rory offers to help the bridesmaids get ready for the ceremony, and is hurt when she learns about Logan's behavior while they were apart. Meanwhile, Lorelai babysits Gigi to help Christopher out, but is appalled by the 4 year-old's terrible behavior and Zach comes to the diner with a surprise for Lane.
After forgiving Logan, Rory decides that she needs time to herself and travels to Stars Hollow for some peace and quiet. However, when she arrives, Rory can tell that Lorelai is upset, but Lorelai refuses to admit that Luke going away with April for a field trip is bothering her. Meanwhile, Zach asks Mrs. Kim for Lane's hand in marriage and is surprised by the deal she proposes and Rory goes to Anna's store to spy on her.
Lorelai has a strange dream featuring singer/songwriter Paul Anka. Rory and Logan are back together but Logan knows that Rory still hasn't forgiven him. To cheer himself up, Logan decides to go on a stunt with the Life and Death Brigade. Meanwhile, Rory travels to Philadelphia to attend Jess' open house for his new store/art gallery/publishing house. There, Rory runs into Luke while on a field trip with April. Back in Stars Hollow, Lorelai is horrified when she finds out that Richard and Emily have been real estate shopping near her town and tries her hardest to get them to dislike Stars Hollow.
With Lane's wedding rapidly approaching, Rory and Lorelai plan a bachelorette party, but their plans end up falling through, as does Zach's bachelor party, so the two groups party together in a parking lot. Later, Lorelai tries to find a date since Luke cannot attend. She tries to get Michel to go with her, but he gets Celine Dion tickets and cannot attend. Rory suggests that Lorelai take Chris, and Chris immediately agrees. Meanwhile, Grandma Kim arrives for the wedding, not knowing that Lane is a 7th Day Adventist, not a Buddhist like she is. After the wedding and several shots of tequila, Lorelai collapses and Christopher takes care of her.
Luke wants to throw April a birthday party and Lorelai eagerly volunteers to help. Luke crushes Lorelai when he tells her that he'd rather she not meet April yet, but is forced to enlist her help when the party turns into a disaster. At the party, Lorelai finally gets a chance to bond with April and turns the party disaster into an instant success. Meanwhile, Logan is rushed to the hospital after a Life and Death Brigade stunt goes wrong and Rory goes to the hospital to be with him.
Rory meets with Kimberly Wells, a Wall Street Journal reporter, concerning an interview that Wells had with Mitchum Huntzberger. Rory wants the reporter to publish a correction to the article that would correct what Mitchum said about her. Emily, after having LASIK eye surgery, asks Lorelai to go with her to a meeting at a real estate office, and Lorelai reluctantly agrees. There, they look at pictures and layouts of several extravagant homes and Emily reveals a surprise she has in store for Luke and Lorelai. Also, Liz and T.J. arrive at the diner after a fight hoping Luke can help them patch things up. Meanwhile, Jackson and Sookie have to get rid of a yard full of marijuana when they discover it was planted in Jackson's fields.
Stars Hollow becomes overrun with troubadours when Stars Hollow's own troubadour is discovered by a record label. Rory, the night before Logan leaves for London, throws a huge party for him, but the wild party is overshadowed by the fact that he'll be leaving the next day. Meanwhile, Emily and Richard attempt to set Christopher up with a beautiful woman during Friday night dinner. Later, Lorelai confronts Luke about their wedding postponement and issues him a tear-filled ultimatum.