Rory has a difficult time settling in at Chilton, struggling to match the demands of private school and attracting the fury of classmate Paris Geller.
The contrasting father–daughter relationships of Emily–Lorelai and Lorelai–Rory become a defining theme of the show.
Series creator Amy Sherman-Palladino has summarised the core of Gilmore Girls: "I think the theme was always family and connection. The ironic twist in her life is that then this daughter that she created this half family for, likes the family that she left.
I always felt like the underlying thing about Gilmore was that, if you happened to be born into a family that doesn’t really understand you, go out and make your own. It was a cycle of crazy family." The series also focuses on both girls' ambition: Rory to attend an Ivy league college and become a journalist, and Lorelai to open an inn with her best friend Sookie St. The romantic relationships of the protagonists are another key feature; throughout the series Lorelai has a "will-they-won't-they" dynamic with her friend, local diner owner Luke Danes, while also harboring unresolved feelings for Rory's father, Christopher Hayden.
Rory has three boyfriends during the run of the show - local boy Dean Forrester, bad boy Jess Mariano, and wealthy Logan Huntzberger.
Luke's teenage nephew, Jess Mariano, comes to live under his care.