So........:
Rory goes to Philadelphia for Jess' works open house. Jess thinks that, by what Rory has told him, she and Logan broke up. So they kiss. But since Rory breakin up with Logan is not true, she pulls away. And Then:

"You came here alone; to Philadelphia." Jess states.

"He was out of town." Rory's is speaking of Logan.

"I don't deserve this, Rory." Jess says.

"No, you don't! You don't deserve it! I just- I'm in love with him. Despite all the bad he's done, I can' help it. I'm in love with him." Rory confesses.

Jess sighs. "Love huh?"

"Yeah." Rory responds.

"I'm so sorry I came here." She says.

"I'm not." Jess responds. "It is what it is. You. Me."

"Thanks Jess." Rory says.

Rory walks out the door leaving Jess behind.

Back in New Haven the next day, Rory sits alone in her and Logan's apartment thinking about yesterday, with Jess. It's not as if it was a big thing, just a kiss. An accidental kiss. No harm no foul right?

But if that were true, what was this she was feeling? Because of the situation, Rory believed it to be worry or guilt. But it felt different, even more familiar. She racked her brain for the answer, but for some reason she couldn't identify the exact feelings.

Rory knew that she could get advice about this most likely from her mother. But with all the problems between her and Logan lately should she tell Lorelei about kissing Jess?

Like what did her letting that happen mean? And what would her mother say? She knew she could easily answer this by picking up the cell phone on the nightstand next to her and dialing her mother's number, but she couldn't help but feel like it wouldn't be such a good idea.

If not Lorelei then who could she confide in?

Logan is defiantly out. Telling him she kissed another guy is most likely the worst thing she could ever tell any boyfriend.

Paris is debatable.

As is Lane.

But she didn't. Instead Rory thought back. Back to two, three, four years ago. She thought about Jess the first time they met. When they were in that car accident. She thought about before they dated and while they dated and after; everything about him that happened up until this very moment.

Doing this she found a few points: when Jess showed up while she was staying with her grandparents, when he told her he loved her then left, when he disappeared before graduation, the time they kissed at Sooki's wedding. And last, but not least, the way she felt when they weren't together. When she was with Dean and Jess was dating that girl, Shane.

Then it hit her. The feelings they all made sense. The familiarity all fell into place. All those times. Jess was the one guy who kept coming back. No matter what happened, over time he came to her. He found her again and tried, showed her that he wanted them to be together.

So then she thought, maybe it was true; maybe it's supposed to be Rory & Jess. Not Rory & Dean or Rory & Logan. But Jess. Maybe it's always been Jess.