So I just recently rewatched the episode where Jess shows up at Rory's apartment at Yale, and I always hated how that episode ended, and that she ends up going back to Dean for a while and then that progression eventually ends her up with Logan, whom I always felt was the lamest of all her boyfriends...but anyways this is my brief sort of oneshot alternate universe solution to the ending of that episode.
Rory stared at her phone. She'd been stewing about this for over a week now, ever since Jess had shown up so abruptly. The terrified 'no' she'd kept throwing at him was still ringing in her head, and she didn't think what'd she'd said was true. A part of her did want to run away with Jess, but mostly she wanted to be with him, not to throw everything she had now away, not to completely uproot her life or his, just to be with him.
Taking a deep breath she dialed Luke's number. If there was any way for her to get in contact with Jess it would be through Luke.
"Hello?" Luke's gruff familiar voice picked up after a few rings.
"Hey, Luke?" Rory said nervously brushing some loose hair behind her ear.
"Rory!" Luke sounded surprised, which made sense as she hadn't really ever had a reason to call him before. "Did you need to talk to your mom? I can go get her?"
"Oh no," Rory cut in quickly, feeling embarrassed and glad he couldn't see her face. "I was just wondering..." She paused not sure how to state what she needed to say. "My mom said you've been in contact with Jess?" She finally managed to blurt out as weird half question.
There was silence on the other line, apart from the business background noise of his diner. "You want to talk to Jess?" He sounded rather incredulous.
"Please Luke, can you just give me his number, if you have it?" Rory tugged at a sleeve nervously.
"Ok, ok, you got a pen with you?"
"Uh-huh, thanks for this Luke." She mumbled into the phone.
He dictated a number to her. "I hope this works out for you; he's turned out to be an alright kid."
Rory hardly knew how to respond to that a quickly hung up the phone.
She stared at the numbers on the slip of paper clenched tightly in her hand. She felt a tremor run through her. It was almost enough to make her go running back to Dean, but he was married and it wasn't fair for her to monopolize him, even if he'd been having troubles with his new wife, even if they were having apparent relationship problems right now.
Trembling she entered the numbers Luke had given her into her phone. Hesitating only a moment more, she pressed the dial button. She found she was a bit disappointed when all she got was the answering machine, but maybe it was better this way.
"Hey – Jess, this is Rory...I've thought about what you said, and I don't think I can run away with, but why would we need to do that to be together anyways? Why can't we be together, but I still get to go to school? Maybe it's a bit of a compromise...but don't you do that for people, well for people that you love? I love you Jess. I love you!" She shouted the last bit and snapped her phone shut, throwing it across the room in terror at what she'd dared to say.
Part of her hoped that Jess never heard the message, but of course another part of her was desperate that he call her back right away.