Picking up on the same night as last season's finale, Lorelai is very upset that Rory has lost her virginity to her married ex-boyfriend Dean. Luke is happy and relieved to learn that Lorelai wants to pursue their new romantic relationship. Meanwhile, after announcing that she and Richard are officially separated, Emily decides to leave immediately for Paris. Realizing that Dean's marriage may not be over after all, Rory agrees to spend the summer in Europe with Emily.
Rory calls Lorelai from Rome and admits that she made a mess of things with Dean. Lorelai gives Dean a letter from Rory, but Dean's wife Lindsay finds the letter and throws Dean out of the house. Rory returns from Europe, and a terrible scene ensues when she and Lorelai run into Lindsay and her mother on the street. Meanwhile, Luke returns to Stars Hollow after many weeks helping his injured sister on the Renaissance Fair circuit. Luke and Lorelai try to find a private spot to say hello, but are interrupted by a town parade.
After Lorelai and Luke spend a romantic night together at Luke's place, Lorelai, walks into the diner early the next morning dressed in one of Luke's flannel shirts, only to discover that the place is full of customers. Lorelai is a little offended when it appears that no one cares about their relationship, until it becomes a topic of heated discussion at the town meeting. Rory has an angry exchange with a haughty, rich student named Logan after he is rude to her friend Marty. Paris holds a wake for her older lover Asher, who died over the summer. Richard and Emily bicker about their separation protocol.
Rory and Dean find it increasingly difficult to be alone together due to their distant living arrangement and the fact that he is sharing a car with his estranged wife. Impulsively, Rory asks Dean if he only left Lynsey because she found Rory's letter, and is not completely satisfied with his response. Lorelai and Sookie run Jackson's campaign when he decides to run against Taylor for Town Selectman. Lane tells her band-mate Zach that she has feelings for him.
Feeling bad that her relationship with Dean has become awkward, Lorelai suggests that she and Luke double-date with Rory and Dean, but the evening turns ugly when Luke is unable to disguise the fact that he thinks Dean isn't good enough for Rory. Meanwhile, Emily and Richard are lonely and a little lost without one another, but neither can take the first step toward reconciliation. Lane is frustrated with her inability to connect with Zack
Lorelai and Sookie are thrilled when author Norman Mailer and a young reporter show up repeatedly in the dining room of the Dragonfly Inn, but Sookie's awe turns to annoyance when Mailer refuses to order any food. Working on a story for the Yale newspaper, Rory uncovers evidence of an intriguing secret society to which Logan belongs. Meanwhile, when Rory's father, Christopher, appeals to Lorelai for help after his girlfriend leaves him to raise their baby daughter by himself, Rory orders him to leave Lorelai alone. Finally, Sookie realizes that she is pregnant again.
Lorelai is mortified at the prospect of Luke interacting with her snooty parents--and Luke soon learns why; Rory participates in a bizarre off-campus event to research a story on Logan's secret clique; Lane and Zack have a stay-at-home first date.
Rory is touched when Emily and Richard throw a party to introduce her to their Yale Alumni friends, but it soon becomes obvious that their ulterior motive is to find her a suitable husband. When Dean arrives at the party to pick Rory up, he realizes he doesn't belong in her privileged world. Meanwhile, Luke cooks a romantic dinner for Lorelai, but their evening is interrupted by a feuding Liz and T.J. Zack is read the riot act by Mrs. Kim, whose intimidation of Kyon also irks Lane.
Rory decides that she and Lorelai should split up at the next Friday night dinner and confront Richard and Emily separately about ending their separation. However, Emily dashes their hopes of a reconciliation by announcing that she is ready to begin dating. Meanwhile, Lorelai invites Christopher for lunch at the inn, unaware that Rory had warned Christopher to stay away from her mother. Feeling guilty that she hadn't told Luke about seeing Christopher, Lorelai confesses that they had lunch, and Luke 'convinces' himself that he isn't jealous. Jackson is overwhelmed by the twin burdens of Sookie's pregnancy and his role as town selectman. Paris tries to observe Ramadan.
Rory is delighted when the headmaster of her old prep school asks her to play hostess to a young student, Anna, who is thinking of applying to Yale. However, Anna turns out to be more interested in boys than academics and runs off to party, leaving Rory to deal with Logan's elaborate practical jokes. Meanwhile, Lorelai and Luke have their first fight when she accidentally upsets him by buying an old boat that had belonged to his father.
Wanting to make peace with Rory, Christopher shows up at Yale, but she brushes off his attempt at reconciliation. When Lorelai learns that Christopher's father passed away, she spends an evening at his place trying to console him, then neglects to tell Luke the truth about where she was. Meanwhile, Emily and Richard are briefly reconciled when they take in a lost dog. Finally, Luke brings Lorelai her own portable skating pond, and the Stars Hollow annual Revolutionary War reenactment takes on a racy new twist.
Rory is bummed when Logan, whom she helped write an article for the Yale Daily, doesn't return the favor by inviting her to be his date at a book signing party thrown by his father. When Richard sees Emily talking to man she dated, he rear-ends her car, forcing her to ride home with him. The Gilmores reconcile and decide to renew their wedding vows. Emily warns Christopher that Lorelai and Luke are getting serious and he had better do something quickly if he hopes to end up with Lorelai.
Talk about bad timing. The night before Richard and Emily renew their vows, Lorelai and Rory feel obligated to throw Emily a bachelorette party. At the ceremony the following day, Rory tells Logan she wants a relationship with him even though he's not ready to commit. Later, when Lorelai, Luke and Christopher discover Rory and Logan together, half-dressed, the shocking scene leads to an angry confrontation between Luke and Christopher. A furious Lorelai figures out that Emily invited Christopher in an attempt to break up her relationship with Luke.
Lorelai is frantic after the disastrous scene at wedding, and begs Luke not to give up on their relationship. However, Luke's decision that he needs time alone leaves Lorelai devastated. Stranded at Yale without her car, Rory is so worried about Lorelai's depressed state that she borrows Logan's limo and driver and heads home to Stars Hollow to care for her mom. Meanwhile, Taylor has the whole town talking sides on the Lorelai/Luke relationship.
When Lorelai discovers that Luke's boat is no longer in her garage, the void she feels without Luke seems even more painful. Luke agrees to build sets for the elementary school's production of 'Fiddler on the Roof,' knowing that Lorelai is the costume designer and hoping that their paths will cross. Meanwhile, Rory and Marty makes plans to spend a day together, but Logan drops by Rory's dorm room and convinces them to come out to dinner. After a terrible evening with Logan's clique, Marty tells Rory how much he likes her, but she admits she has a crush on Logan.
When Richard and Emily return from their second honeymoon, Rory attends Friday-night dinner without Lorelai, who refuses to speak to her mother or see her, and plans a girls' night out with Sookie instead. Richard and Emily then give a 100-year-old Greek book to Rory and have yet another maid. Rory surprises everyone with a rare outburst at her grandmother for interfering in Lorelai's love life. Meanwhile, Luke, who's miserable without Lorelai, takes his anger out on his customers and his dark mood causes him to burn the food and when one customer wants his omelet redone, he throws him out of the diner. When a meter maid is writing a ticket to put on Luke's boat (that is parked in front of the diner) Lorelai comes in time to put some quarters in the meter. Emily goes to the diner to talk to Luke. Meanwhile, Lane has a horrific realization about her mother's influence.
Rory regrets her agreement with Logan that they can date other people after she sees him out on the town with another girl. Later, at a party where everyone dresses as a character from a Quentin Tarantino film, Rory shows up with Logan's friend Robert, forcing Logan to admit his jealousy. Meanwhile, now that Lorelai and Luke are happily reunited, Emily can't understand why Lorelai still refuses to show up at Friday night dinner. Emily's second visit to the diner to speak to Luke leads to a bitter mother/daughter confrontation. Finally, Michel appears on 'The Price is Right' and wins a motor home.
When Stars Hollow's oldest resident dies and leaves his house to the town, Luke has an ulterior motive for volunteering to help turn the house into a temporary museum. Dean is also working on the project, and offers Luke some unwelcome advice about the dangers of dating a Gilmore girl. To get publicity for the Dragonfly Inn, Lorelai does an interview with a travel magazine, but immediately regrets the unkind comments she makes about being raised by Emily. Meanwhile, Lane suspects that Zach is having a fling with music store owner Sophie, while Rory and Paris are both devastated by trouble with their respective boyfriends.
After Rory tells Logan that she can't have a casual relationship with him and they should go back to being just friends, she is amazed when Logan insists he is ready to commit to her. However, when he brings her home to meet his powerful and intimidating family, Rory is shocked by his parents' negative reaction to the relationship. The following day, Logan's father apologizes to Rory and offers her an internship at one of his newspapers. Meanwhile, when Sookie is put on bed rest by her doctor, Lorelai calls Luke to fill in as the substitute chef at the Dragonfly Inn.
Wanting to make a good impression on Logan's powerful father, Mitchum Huntzberger, Rory learns everything she can about him before starting work as an intern at one of his newspapers. When Lorelai learns that Emily and Richard have invited Logan to Friday night dinner, she ends her boycott of family gatherings in order to get to know Logan better. During the evening, Emily and Richard fawn over Logan, but Lorelai sees a side of him that causes her to worry about Rory's involvement with the Huntzberger family. Meanwhile, Lorelai gets an interesting job offer, and Luke tries to talk Taylor into closing the Stars Hollow museum.
Rory is surprised by the performance review she receives from Logan's father, Mitchum Huntzberger, at the newspaper. Luke's plan to buy the Twickham house is threatened when Kirk makes a competing bid. Lorelai is thrilled when the travel magazine featuring The Dragonfly Inn hits the stands, but worries about Emily's reaction to the article. Meanwhile, Sookie goes into labor and Emily becomes a personal patron for a ballet dancer.
Rescuing Rory after a night of reckless behavior with Logan, Lorelai is shocked to hear her daughter's plans for the future. Lorelai first turns to Richard and Emily for help, but soon realizes that Luke is the only person she can trust.