This starts during "Rory's Dance", Season 1, Episode 9. It deviates quite heavily from the actual storyline from here, as you will see ;) Assume that everything up until when this starts is the same. I'm assuming it takes place in mid-December 2000.

While Rory was reading poetry to him, Dean started kissing her. While she was distracted he took her book from her and placed it on the floor. He pulled away and stood up, pulling her to her feet. He held her, kissing her more passionately now, pulling her close to him. He pulled away, quickly pulling a few of the yoga mats onto the floor.

"Uh Dean, I don't think…" Rory started nervously, but Dean kissed her before she finished. She kissed him back passionately, letting him lead her towards the mats. He pulled away, sitting on the mat looking up at her and pulled her down gently by her hand he was holding.

As he kissed her, Rory got distracted again, kissing him back passionately, but when she realized what was happening she tried again. She pulled away, "Dean, I don't…" Dean went back to kissing her, kneeling over her and gently lying her down. She could feel his hand pushing up her dress but continued kissing him.

Everything happened the same, although Rory feels guilty denying that anything happened, given that it did. The following happens in April 2001, I figure between season 1 & 2, so they are back together.

Rory started to panic. No. There was no way. They'd only done it once. She tried to think, had she had her… monthly visitor… since then? She had been so busy studying, trying to keep up with all of the school work at Chilton. The newspaper. She'd been so busy. Rory tried to take deep breaths. She looked up and realized everyone was starting to leave the room.

Instead of going to lunch Rory walked out of the school. She couldn't think. She started pacing out the front of her school gate. Then the obvious answer came to mind. She needed to take a test. Normally she liked tests but this was one she didn't want to take. She took a deep breath and went to the nearest pharmacy to buy pregnancy tests to see if her worst nightmare was coming true. As soon as she got them she raced to the bus stop. It felt like hours before the bus arrived, but she knew from constantly looking at her watch that it had actually been 14 minutes.

When she got home she raced to the bathroom to take the tests. She glanced uneasily at the cups that came with them, but filled one from each packet as instructed. She then placed one of each brand of stick in each cup, just in case. She then started pacing. 6 minutes, that's how long they were going to make her wait to find out what she already knew, but was not willing to admit fully until she saw the positive tests. What was her mom going to say? She would be angry, of course she would be angry. The one thing she told her not to do. Do not get pregnant, do not follow in your mother's footsteps. She loved her mom. She was proud of her mom and how amazing she was. She couldn't have asked for anything more from her. She was going to be so disappointed. I'm supposed to go to college. I'm supposed to finish high school first, I guess, how am I going to finish high school?

This can't be happening. It was only one time. Why did she keep coming back to that? She knew it could happen even if you only did it one time. She knew she shouldn't have done it that one time. Pregnant. At 16. Just like her mom. She'd sullied the Gilmore name, just like her mother. Her grandparents, they'd be so angry too. Sookie would be disappointed as well, although she didn't think she'd care too much. Oh no. Dean. How do I tell Dean? This affects Dean too, doesn't it? She supposed it hadn't affected her father too much when her mother had gotten pregnant. But Dean was different. Dean would be there for her. He loved her. He'd said so, more than once. Rory started to breathe a little easier. Maybe he could even help her tell her mom. She kept glancing down at her watch and saw it had still only been 4 minutes. She figured they were probably already showing that she was pregnant but she wasn't ready to go and look yet.

What was she going to do? She paced for another 2 minutes, the same thoughts running through her head. She had disappointed everyone. She had let them all down. They all believed in her. She braced herself and slowly walked into the bathroom to see the tests. The 4 tests sitting there, every one of them telling her what she already knew. She was pregnant.

Rory took a deep breath. Dean was still in school for another hour. She paced around the house for about 10 minutes and then started walking aimlessly around town waiting for school to finish. When it did she was there, waiting for Dean.

When he saw her, Dean smiled widely. He hugged her and started kissing her. Enjoying it, Rory kissed him back passionately before remembering what she had to tell him. She started pushing him away and pulled away from the kiss. "Wait I need to tell you something." She said firmly.

"Can't it wait?" Dean asked impatiently.

"Umm, not really." Rory replied getting nervous again.

Dean sighed. "What is it?"

"Come back to my place with me." Rory said grabbing his hand and pulling him along before he had a chance to answer.

Seeing that Rory was in no mood to be argued with, Dean let her lead him back to her house.

After they entered her house, Rory turned to face Dean and took a deep breath. "I… I… I'm pregnant." Rory finally managed to stammer.

"What?" Dean shouted, half shocked, half angry.

"I'm pregnant." Rory said a little louder and more firmly.

Dean looked at her stomach but couldn't see anything with her baggy top. "You have to… get rid of it!" Dean yelled, towering over her.

"I can't... I couldn't do that, Dean." Rory whispered quietly.

"My parents can't know about this, I can't raise a baby. Rory, we can't do this." Dean stated loudly.

"I have to. My mum did. I can. I just... can't tell her. Oh man. She would kill me. I don't know what to do. Please Dean, I need your help." Rory pleaded.

"If you don't… take care this… don't come near me again, I don't want anything to do with... this." Dean said firmly, gesturing towards her stomach, stalking off towards his house.

Rory couldn't stop crying. She figured it was probably too late for what he was asking her to do now anyway. How long had it been? 4 months? It didn't matter anyway, she couldn't… kill her baby. Rory started panicking not knowing what to do. She ran to her room and started emptying out her money box. $327.45. She knew that wouldn't last long. She felt her baby kicking on the inside and pressed her hand to her stomach to feel it on the outside too. She took a deep breath as she scribbled a note to her mother saying she was staying at Lane's house tonight.

She ran back into town and hovered around Lane's house while she waited for the bus. When she saw the bus she hurried to catch it and quickly got on, hoping no-one would see her. She paid her fare and walked to the back of the bus, slumping in a corner seat. She pulled out her phone and turned it off.

Rory went to her grandparents' house. She had to get out of town. Just in case anyone had found out. She couldn't be around when her mom found out. She pressed the doorbell and the maid answered. "Hi, I'm Rory, uh, the granddaughter."

Emily heard her granddaughter's voice at the door and rushed to meet her. "Rory! It's lovely to see you. What are you doing here? Come in, come in." It was then she saw the distressed look on Rory's face.

"I, uh, needed to get away from mom for a bit. Can I stay here tonight?"

"Of course, come in." She said pulling her into the living room. "We should call your mom though, let her know you're alright."

Rory panicked. "No!" She said quickly. "I told mom I'm staying at a friend's house tonight. She knows I'm ok. Please don't tell her I'm here." She pleaded.

Emily watched her granddaughter carefully. She figured the girl didn't want to be caught out in a lie and her distressed state upon arrival was to do with a fight she'd had with her mother. "Well, ok. Would you like a drink?"

"No, thank you, I'd really like to just go to sleep. If that's ok?" Rory asked hesitantly.

Just then Richard walked into the room and noticed Rory sitting there. "Rory! It's wonderful to see you. What are you doing here?"

"She wanted some time away from her mother." Emily explained smugly.

Richard chuckled slightly. "Well, you're welcome here anytime."

Rory fidgeted uncomfortably. "Is it ok if I go to bed now?"

"Oh. Yes. Of course." Richard said a little hurt that she didn't want to spend time with them. It was still early, they hadn't even had dinner.

Emily showed Rory to one of the guest rooms and gave her a nightgown to wear. Rory quickly changed and crawled into bed and, demonstrating just how tired she was, she slept until 6 the following morning. She had been wondering if she'd be able to sleep at all with all of the thoughts floating around in her head.

The next morning Rory found her clothes on the dresser, where she had put them the night before, but they were freshly cleaned and pressed.

Rory walked down to breakfast and saw that there was a huge feast waiting to be consumed. There were all kinds of fruits, cereals, muffins, pastries. Her grandfather was reading the paper, her grandmother just sat eating a piece of grapefruit. "Help yourself to anything, do you want something else? Eggs? Pancakes? The maid will make you anything."

Ordinarily Rory didn't like to inconvenience anyone, but she didn't know when she'd next be able to get a decent meal. "Could I have eggs, bacon and pancakes, please?"

Emily just smiled at Rory's eating habits. They reminded her of Lorelai when she was younger. "Certainly. Greta! Greta! Prepare Miss Gilmore some eggs, bacon and pancakes." Emily instructed.

As soon as Rory had finished her breakfast she explained that she had to leave to get her uniform and go to school. She hugged both of them tightly, wishing she'd had the chance to do the same with her mother before she left.

Rory caught a bus to New York and saw that she had arrived at 11:13. She found a map and looked for a town that looked like it might be what she was looking for. She knew she wanted to go south, but where? Then she saw it, 'Silveroak.' She found an internet kiosk and did a search on the town. She couldn't find much, but from what she did find she figured it would be what she was after. She figured out how to get there and went to board the bus that would take her most of the way there, from where she could catch a connecting bus to her town.