Lots of relationship conflict.
Gilmore Girls Season 3 furthers the relationship conflict from Season 2. We see Rory & Lorelai struggle with Christopher's big news. He announced at Sookie's wedding that Sherry was pregnant, right when things finally started to look like he & Lorelai were going to get together. Rory has to deal with being loyal to her mother while still being supportive of her dad's decision.
Through all this, Rory has her own relationship issues during Gilmore Girls Season 3. She tries to convince herself that Dean is the perfect boyfriend while she is still attracted to Jess. She never wrote to Jess during her summer away at Washington D.C. She comes back to Connecticut to find that he is dating someone else. She pretends that it is no big deal because she is still dating Dean. Dean even forgave her when she was in a car accident with Jess & they totaled the automobile that he built with Rory. Jess even gets his own car & no one can figure out exactly how he afforded it, not even Luke. This all comes to a head in the episode "They Shoot Gilmores, Don't They?" This is an annual dance marathon that Stars Hollow holds. Kirk always wins & Lorelai is gunning for his spot this year. Unable to find a suitable partner, she talks Rory into dancing with her.
Sookie & Jackson experience their first year of marriage during Gilmore Girls Season 3. Sookie becomes obsessed with decorating her home with a manlier decor that Jackson hates. Jackson brings up the idea of 4 in 4, which is four kids in four years, much to Sookie's surprise.
Paris Gellar makes a lot of appearances in Gilmore Girls Season 3. She starts to see Jamie, a good looking college student. This mellows her out a lot & she even confides in Rory. Then there is drama on the student council & they are back to being bitter rivals.
Gilmore Girls Season 3 is pivotal because it's the season where we find out if Rory gets into Harvard. We even discover if she really wants to go there or if she has her eyes set on somewhere else. Lorelai has a big career change heading her way when the Independence Inn starts on fire. Rory also has to find a way to pay for her college & mend a rift that Lorelai created with Emily & Richard.
Gilmore Girls Season 3 leaves us wondering if Jess is really out of Rory's life for good. The Gilmore Girls have a new college to look forward to. The show has really been leading up to the point where Rory graduates. The season finale is satisfying & doesn't leave the audience with such turmoil the way that it did in Season 2.