This is my take on how things could have happened in Swan Song (3.14). In my version Jess arrives on time. The three of them make small talk, then the eat dinner, and Jess takes Rory home.
"We're here." Jess smiles as he pull into Rory driveway.
"Yes we are. I'm sorry I accused you of getting in a fight with Dean."
"It's ok."
"But I still can't believe a swan attacked you." Rory says as she throws open the door.
"I know but it really did happen."
"So what do you want to do?" Rory asks after throwing the house keys onto the coffee table.
Jess doesn't say anything. He leans in and kisses Rory. Jess pulls away.
"What?"
"Rory maybe we should slow down."
"No I don't want to."
"Are you sure? It's ok with me if you want to."
"No I want to do this."
"You're sure."
"Yes."
"With me? Tonight?"
"Would you just shut up."
Jess complies and they resume their prior activities. They end up on the couch. He's gentle and considerate the entire time. Rory is calm and relaxed. Afterward they both fall asleep.
The next morning:
Rory rubs her eyes and rolls out of the sun. When she opens her eyes all of the way she sees Jess lying on the couch next to her.
"Jess you have to get dressed."
"Why?"
"Because my mom will be home soon."
"She won't be home for another 2 hours." Jess points out before kissing her.
"Jess stop."
"Are you sure you want me to stop?"
Rory doesn't verbally reply she simply leans back in and kisses him. Some how they end up repeating the process from the night before.
"Jess you really have to get dressed now."
"Why?"
"Because if my mom catches us she'll kill us."
"Ok." Jess gets dressed and leaves quickly.
Lorelai returns a few hours later:
"Daughter where are you?"
"Hi mom." Rory greets Lorelai at the door.
"So how was your dinner?"
"It was fine."
"Did your grandmother behave?"
"Yes she did."
"Good I'm glad."
"So what did you and Jess do last night? Babette said that Jess didn't leave until this morning."
Lorelai had given Rory a chance to come clean. Even though Rory agreed to tell her mother these kinds of things she felt to guilty to so she lied.
"We just watched movies, until we fell asleep."
"Ok." Lorelai believed Rory her innocent daughter.
"I'm going to go get a book from Jess.
"Can't it wait I just got home and I'm hungry."
"I'll pick up food on the way. I just want to look at it for school."
"Ok."
Rory goes into the diner passes Luke and whizzes up the stairs to find Jess.
"Hi!"
"Hi we need to talk."
"Ok. About what?"
"Jess we shouldn't have let last night happen."
"Rory you were fine with it last night... and this morning."
"I know, but please just keep it to yourself I don't want my mom to know."
"Who am I going to tell?"
"I don't know. Oh and I need to borrow a book."
"Which one?"
"Something that I would theoretically need for school."
Jess throwsa book at her and she leaves to go to Al's Pnacake World. Rory is over come with guilt but knows better than to tell her mother.