Part 2
Jess interacts with Rory to get what he needs, but he also keeps her at arms length because he does not trust her. They both like each other as people and Rory wants to be friends, but Jess won't let her in right away. They'll both also call each other out on bad habits and behavior, though more Jess than Rory at first.
Over time, Rory begins to earn Jess' trust and Jess expands Rory's view of the world and her place in it. She finds out that Jess is on his own and homeless.
They are attacked while driving in a car by the people that are after Jess and took his parents, where Jess saves Rory because they want to kill her for what she knows and to get rid of any witnesses. The attack was also made to look like an accident.
Jess tells her the truth after this and asks for her to tell him what she knows so he can save his parents. She tells him and decides to help him rescue his parents and stop the government organization. Rory and Jess officially become friends.
They do some investigating together, as well as individually and comparing results. Rory finds out that Luke and Rogue are siblings and tells Jess. Jess also teaches Rory some survival skills and self-defense. As a cover, Rory says that she's tutoring Jess.
Star Hollows thinks that Jess is a bad boy out to cause trouble, and Lorelei and Dean don't want him near Rory. However, Rory keeps hanging out with him because he's her friend, it took a long time to earn his friendship and trust, and she wants to help him. Eventually, Jess becomes friends with Lane and Paris through Rory, but it takes a lot of time.
P.S. There is no love triangle for plot reasons, but people can assume that Jess is trying to steal Rory for himself.