Lorelai and Chris begin to date. Christopher forgives Sherry after she sends him a letter apologizing. Rory returns to Yale for the fall semester of her senior year. April is staying with Luke temporarily while her mom, Anna, is out of town. Richard starts at Yale as a guest lecturer. Rory covers an art exhibition for the Yale newspaper and meets her new friends, Lucy and Olivia.

Lorelai and Chris fly to France to take Gigi to see her mother, Sherry. Once there, Chris proposes to Lorelai and the couple return to Stars Hollow as Mr. and Mrs. Hayden. The joy of Rory's trip to the country (Stars Hollow) with Lucy and Olivia is dampened by Rory's breakdown regarding her fears for the future, and the unexpected appearance of a past friend who disavows having known Rory. Zach and Lane find out they're having twins and break the news of their impending parenthood to Mrs. Kim, with unexpected consequences.

Rory is angry that she could not attend Lorelai and Chris's wedding. Logan is moving from London to New York City. He and Rory fight about an article she wrote. April develops appendicitis and Luke takes her to the hospital.

Chris and Lorelai tell Emily and Richard about their marriage. Lorelai becomes determined to make Christopher liked by the people in Stars Hollow. Anna tells Luke that she is moving across the country and taking April with her, in which Luke tells Anna he will fight for custody. Rory moves in with Paris, after moving out of Logan's apartment. She attends a party at Lucy's apartment; Marty reveals to Rory that he still has feelings for her. Luke's evident feelings for Lorelai are still apparent in his behavior.

Luke and Lorelai share a moment when Luke introduces her to Liz's new baby, and Christopher witnesses the scene. Lorelai and Christopher get into a fight over what Lorelai wants versus what Christopher wants. Luke contacts a lawyer over his custody troubles with Anna. Christopher and Luke fight in the town square. Logan discovers that Rory and Marty have been pretending that they just met, and he reveals the truth to Lucy. Emily gives Lorelai advice about her marriage.

Rory makes amends with Lucy while Christopher finds the letter Lorelai wrote for Luke's character reference. Rory witnesses a frightening sight while at Richard's Economics class. Sookie is acting weirdly so Lorelai makes Jackson confess: Sookie is pregnant again, even though Sookie told Jackson to get a vasectomy.

Lorelai tries to reacquaint herself and Luke by visiting the diner, but the reunion results in an awkward silence. Paris freaks out over too many opportunities when she gets accepted to a quite a few graduate programs. Rory's hopes get squashed when she gets rejected for the internship at the New York Times. While staying with Lorelai, Jackson accidentally destroys her dollhouse.

At Rory's graduation party at her grandparent's house, Logan proposes to her. Emily and Richard sing Rory a graduation song. Rory is caught off-guard and says she needs time to think about it. After Rory graduates from Yale, she tells Logan that she can't marry him. Logan tells her it's all or nothing and Rory decides to decline. Logan ends their relationship.