Part 5
Jess decides to stay with Luke, and they slowly become close, with Jess learning to trust Luke, as well. After he is given the appropriate legal status, Jess either attends high school to finish his education or gets his GED. Stars Hollow and Lorelei have mixed feelings about Jess due to his background, which does get him some sympathy. Lorelei and Jess may warm up to each other over time. Jess meets Rory's grandparents at some point, and he and Richard get along very well.
Luke also bonds with his sister again and has interesting, kind-of-macho-but-still-reserved interactions with Logan, especially in the early days when they do meet. Other X-men occasionally travel through Star Falls sometimes, which usually involves some kind of adventure.
Rory doesn't get into Harvard, and she's wait-listed for Yale, but she does apply to other schools, at least ten total, and decides to go to NYU, maybe with a scholarship or grant for some or all expenses. Jess also goes back to New York at some point to get to spend time with his parents after they settle some, probably at the mansion. She and Jess become roommates.
Rogue and Logan get married later, and maybe have more kids in the future.
Bonus Notes:
1. Could be pre-Romance or Just Friends with Rory and Jess depending how the story goes.
2. Rory skips school at one point when helping Jess. When her mom brings it up later, Rory points out that she told her she could leave school for a guy in a motorcycle.
3. When Jess and Dean first meet, Dean tries to intimidate Jess, who just stares back at him until Dean starts to get uncomfortable and leaves.
4. Dean approaches Rory afterwards to apologize and maybe try to get back together; she says no, and they get closure.
5. Dean may end up kind of friends with Jess (kind of a parallel to Logan and Scott) after some other experiences, and maybe anger management.