Rory is pleasantly surprised when her former boyfriend Jess appears at her grandparents’ house and reveals an amazing development in his life. Rory agrees to go to dinner with Jess, but 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.
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Lorelai and Luke begin making plans for their future, but Luke is embarrassed when word spreads that Lorelai was the one who proposed marriage. Still hurt that Rory has decided to drop out of Yale and move in with Lorelai's parents, Lorelai tells them that they can take care of Rory from now on. Although Richard hires a respected attorney and longtime friend to help Rory get an easy sentence for stealing the yacht, a judge orders Rory to serve 300 hours of community service. Logan hosts a "felon party" for Rory.
Rory begins to work 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 home or buy the Twickham house, which Luke has always admired. Luke's sister, Liz, begs him to hire her husband, T.J., as a contractor. When Rory surprises Luke with a 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 to cater Lorelai's wedding, Sookie pressures Lorelai to set a date but cannot get her to 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 goes back to Yale, forcing Rory to confront her true feelings about quitting college. Lane and her band come home after spending their summer performing out of town. 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.
Lorelai misses Rory and tries to call her but soon discovers that her daughter's cell phone is no longer in service. Sookie asks Lorelai and Rory to be the godparents to her two children, hoping they will reconcile when they see each other at the ceremony. However, mother and daughter end up fighting when Lorelai realizes that Rory gave 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 enlists Richard's help in settling the insurance claim. She also needles him about the fact that he has been unable to get Rory to return to Yale. Although he's annoyed with Lorelai, Richard admits that Rory is not doing what she should be doing.
Richard tries to gather information from Logan about Rory's future plans, but Logan mistakenly thinks that Richard is asking when he plans to marry Rory. Lorelai supports Taylor's plan to change all the Stars Hollow street names back to their original historic ones, until she learns the disgusting former name of the street on which the Dragonfly Inn is located. Rory makes a surprising confession to Logan. Richard finally admits that he should have never allowed Rory to drop out of Yale and shows up at Lorelai's house to discuss the matter.
As Rory's 21st birthday approaches, both Lorelai and Rory are saddened that their estrangement will keep them from spending the day the way they had always planned. Richard tries to convince Lorelai to help him concoct a plan to get Rory to return to Yale, but Lorelai insists that Rory has to make the decision herself. Meanwhile, Emily plans an elaborate birthday party. Later, Emily and Richard are shocked when they realize that Rory and Logan have been having sex. Former Secretary of State Madeline Albright appears in a cameo role as herself.
Rory is pleasantly surprised when her former boyfriend Jess appears at her grandparents' house and reveals an amazing development in his life. Rory agrees to go to dinner with Jess, but 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 Rory's dad illuminates issues of trust between Lorelai and Luke. Later, when a person from his past shows up in Stars Hollow, Luke has no idea how to tell Lorelai. After months of estrangement, Lorelai and Rory make their first move towards reconciliation, and Rory takes major steps to change the direction of her life.
After a long absence, Christopher Haden, Rory's father, reappears in the lives of Lorelai and Rory. Luke struggles with what the presence of Christopher will mean to him and his relationship with Lorelai. Lorelai and Rory enjoy their first Thanksgiving at the Dragonfly Inn, and Rory receives surprising news about Logan. Meanwhile, on the eve of an important gig for the band, Lane has to deal with Zack'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, 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 tries to avoid running into Logan. However, when Logan shows up at her apartment and declares his love for her, Rory breaks down.
Knowing he has let too much time go by, Luke is still unable to tell Lorelai about the existence of his 12-year-old daughter, April, and he is thrown into a panic when April wants to hang out with him at the diner. When April and Lorelai both show up at the diner and begin chatting, April innocently explains that Luke is her father. Lorelai tries to be supportive, even offering to postpone the wedding date, but Luke's reaction to this idea leaves her confused and hurt. Back at Yale, Logan takes unusual steps to win Rory back, and the newspaper staff rebels against Paris' reign of terror at the Yale Daily News. Meanwhile, Stars Hollow holds its annual Winter Carnival, and Lorelai and Rory run a booth featuring their dog, Paul Anka, as a fortuneteller.
While Luke deals with the reality of having his daughter, April, in his life, Lorelai tries to pretend she doesn't mind the repercussions the new situation is having on their engagement. Rory's concern over Paris' lack of management skills at the Yale Daily News finally reaches a crisis point when most of the staff quits in protest. With Logan's help, Rory makes a valiant attempt to get the paper out on time. Meanwhile, Lorelai breaks the news to Richard and Emily that their money will no longer be needed for Rory's education, and the resentment starts to build. The subsequent Friday night dinner erupts into an emotional confrontation where all four Gilmores finally get their issues out on the table.
Wanting to get to know her future son-in-law better, Emily asks Lorelai to invite Luke over for dinner. In order to avoid an argument, Lorelai purposely fails to mention that the wedding has been postponed. Meanwhile, the Yale Daily News staff finally fires Paris and chooses Rory to be the new editor. After a furious Paris kicks Rory out of the apartment, Rory has no idea where to go until Logan convinces her to move into his apartment. When Rory gives Christopher a tour of Yale, he learns of the new living arrangement and tells Lorelai.
As Valentine's Day approaches, Rory and Logan invite Lorelai and Luke to spend a weekend with them at Logan's family house on Martha's Vineyard. Rory and Logan have a wonderful time, but Lorelai is upset by Luke's unfriendly attitude towards Logan. Luke's attitude changes when he realizes he forgot to buy Lorelai a Valentine gift, and Logan saves the day by letting Luke give Lorelai one of the gifts he had bought for Rory. When Lorelai finally confesses to Luke that she is worried the wedding will never take place, he reassures her that they will get married soon. The weekend ends in an ugly scene when Logan's father, Mitchum Huntzberger, arrives and berates Logan for ignoring his responsibilities in the family business.
Proud parents Lorelai and Christopher attend a journalism panel at Yale, where Rory dazzles the crowd. Afterwards, Lorelai offers to help Christopher by baby-sitting his 4-year-old daughter and is horrified by the toddler's terrible behavior. The next day, Rory and Logan attend the wedding of Logan's sister, Honor. While helping the bride and her three bridesmaids get ready, Rory is devastated to learn how Logan spent his time during their recent breakup. Logan tries to defend his actions, but a devastated Rory turns to Lorelai and Paris for comfort. Also, Lane is still heartbroken over Zach--until he turns up at the diner with a surprise.
After forgiving Logan for his indiscretions, Rory needs some time for herself, so she visits Lorelai in Stars Hollow. Although Lorelai refuses to admit that she is upset, Rory can tell that she is bothered by the news that Luke will be gone for a few days on a field trip with his daughter. Against Lorelai's wishes, Rory goes to the store owned by the girl's mother, Ana, to spy on her. Meanwhile, when Zack finally works up the courage to ask Mrs. Kim for permission to marry Lane, he is surprised at the deal she makes with him.
Lorelai has a bizarre dream about singer/songwriter Paul Anka (himself). Meanwhile, although Rory and Logan are back together, Logan is miserable knowing that Rory hasn't really forgiven him, and he takes off with his friends for another stunt with the Life and Death Brigade. Rory accepts Jess' invitation to attend an open house at his new book store/art gallery/publishing house in Philadelphia. While there, she is surprised to run into Luke, who is accompanying his daughter, April, on an academic field trip. Back in Stars Hollow, Lorelai is horrified to find that Richard and Emily have been looking at real estate in her town.
On the night before Lane and Zach get married, Lorelai and Rory's plans for a bachelorette party go awry, as do the plans made by Zach's buddies, so the two groups end up together for a makeshift party in a vacant parking lot. Meanwhile, Mrs. Kim tells Lorelai to bring an escort to the wedding. Since Luke is still out of town, Lorelai invites Christopher to be her date. Everyone attends two wedding ceremonies--one Buddhist and one Seventh Day Adventist--followed by a wild wedding reception in the town square.
When Luke prepares a birthday party for April at the diner, Lorelai volunteers to help but is hurt after Luke explains that he still thinks it's too soon for April and Lorelai to meet. Luke changes his mind, however, when the party is a disaster, giving Lorelai a chance to bond with April while turning the event into a huge success. Meanwhile, Rory rushes to be with Logan at the hospital after he is seriously injured during a stunt with the Life and Death Brigade.
Temporarily unable to see after minor eye surgery, Emily enlists Lorelai's help as her driver and companion, finally revealing a surprise that catches Lorelai completely off guard. Meanwhile, Rory takes charge of Logan's recovery when he is released from the hospital. And Luke helps his sister Liz and her husband, T.J., deal with Liz's pregnancy.
On the evening of Logan's graduation from Yale, Rory throws him a wild party, but the knowledge that he is being forced to leave for London the next day makes their time together bittersweet. Meanwhile, at a Friday night dinner, Emily and Richard attempt to introduce Christopher to an attractive young woman. And realizing that she was wrong to let Luke postpone their wedding for so long, Lorelai delivers an ultimatum. Also, Stars Hollow is suddenly overrun with musicians when news gets out that the town's regular street performer, the Town Troubadour, has been "discovered." SONIC YOUTH, SAM PHILLIPS, MARY LYNN RAJSKUB, YO LA TENGO, SPARKS, JOE PERNICE and DAVE GRUBER ALLEN perform.