This is another John x Dean. I know a lot of you don't care for this ship, so if you don't, don't read it.
Suggested by: PrincessPeach211 I deviated from what you suggested a tiny bit, but it's the same basic story line.
As I packed a small suitcase, I happened to look down at my small baby bump. The last five months have been a roller coaster ride.
~Then~
Someone was next to me when I woke up. I could feel their presence. Slowly, I turned to look. It was my dad. I was suddenly aware that we were both completely naked. Dad stirred and slowly opened his eyes. He didn't seem mad, like I expected; it was quite the opposite. He seemed to be happy with our current situation. "Morning" he whispered.
"What happened?" I immediately asked, cutting to the chase.
"Isn't it obvious?" Dad asked.
"Well, yeah, but why?"
"It was something we both wanted, at least at the time. Why? Are you sorry it happened?"
"No, I'm not sorry. It's just... I never expected to ever wake up like this" I explained.
A few weeks later, I found out that I was pregnant. There was only one person I'd had sexual relations with in that time frame. It had to be my dad's baby. My mistake was waiting too long to tell Dad.
I finally told him when I was four months along.
"Dad, I have something... important to tell you"
"What is it, Son?"
"I'm pregnant" I blurted out.
Dad looked shocked, "How long?" he whispered.
"About four months"
He sighed, "I need to ask, is it mine?"
"You've been the only one" I told him.
"Come here" he said, holding out his arms. I went to him, his arms wrapped around me. "We'll figure this out, I promise" he told me.
Over the next few weeks, Dad took care of me. He took care of me better than he ever had in my entire life. Then he made one mistake that made my entire world come crumbling down around me.
I was washing the dishes. Dad suddenly came up to me and said, "Dean, you need to promise me a few things"
I looked up at him, "Of course, anything"
"You need to have this baby. Please, I beg you, have this baby and raise him or her right. I need you to be a better father than I am"
"Okay, but, Dad, why are you talking like this? Is everything okay?"
He nodded, "Everything's fine. You'll be fine" Then he walked away. I was incredibly confused, not to mention worried, but if anyone knew my dad, it was me, so I knew that I needed to leave him alone right now and talk to him later.
I only waiting until I was finished with the dishes to follow Dad. It had only been a few minutes, but I was already too late. I saw him collapse to the floor in our bedroom. Ironic, considering this is where this whole mess started. I knelt on the floor beside him. "Dad?" I asked, not wanting to believe what my mind was telling me. I reached out and shook him. There was no response. "Dad?" I repeated. My voice cracked as I held back the tears threatening to flow. I knew it. He wasn't breathing, there was no heartbeat. He was already gone when he fell. When I stood up, I noticed the piece of paper on the bed. Through bleary, tear-filled eyes I read:
Dean-
If you are reading this, then you found me. There is a reason for my death. It was to save you. I found out that our baby was going to kill you. There was no way for you to survive. I couldn't lose you, and I couldn't ask you to kill that child. So I did the only thing I knew I could. I made a deal, my soul instead of yours. Some may see it as a bad, or even stupid, decision, but it was worth it for you and our child to live. I love you
-Dad
I wiped away the tears that fell. The old bastard sold his soul, just so I could live. I quickly called Bobby so he could help me with Dad. We gave him a proper hunter's burial, just like he would've wanted. "Are you going to be okay?" Bobby asked.
"Yeah, I'll be fine"
~Now~
At the time, I believed that. I thought I could swallow the feelings I had and not be affected by Dad's death. Apparently I was wrong. Over the next couple days, I stopped caring. I stopped caring about the baby inside of me, I didn't even care about myself enough to eat properly, if at all. Now I need to go to Stanford. I need to find Sam. He's the only family I have left, and we need to stick together.
When I arrived, I asked where Sam was living. I found this dorm and knocked on the door. The door was opened by Sam, who seemed shocked to see me as he asked, "Dean?" Before I could say anything, everything went black.
I woke up in Sam and Jess' bed. They were both standing over me. "Are you okay, Dean?" Sam asked. I slowly sat up and waited for the dizziness to leave.
"How'd I get here?" I asked.
"You collapsed, so Jess and I carried you to our room to wait for you to wake up. What's going on, Dean?"
I sighed before explaining, "Look, I'm pregnant. It's Dad's baby, and he found out that the pregnancy was going to kill me, so he sold his soul to save me." Tears burned my eyes and my voice cracked as I continued, "He's dead, Sammy. He's dead, and it's my fault" Sam sat on the bed next to me, and I collapsed into his arms. I tried to hold back the sobs, but they came anyway. He soothingly rubbed my back and let me cry.
"It's not your fault, Dean. He made his own choice. He thought he was doing the right thing"
"I know, but it's still hard"
Sam was quiet for a second before asking, "Why did you collapse, though?" As if on cue, my empty stomach growled. "Oh Dean, please tell me you're eating" Sam begged.
I shook my head, "I can't"
"You have to. If you starve, the baby does, too" I thought about what Dad told me. I need to take care of this baby.
"How about we go out to dinner and catch up?" I suggested.
Sam nodded, "Yeah, it's been a while"
Before we left, I told Sam, "Promise me something"
"Anything"
"Please be there for me"
"Always. I'm going to be around you for the rest of our lives"
"Thanks, Sammy"