I'm going under the assumption that The Amazing Spider-Man was set in 2012, and that Peter was 15 then.
Chapter 1: We've Both Made Mistakes, Haven't We?
September 16th, 2000.
One Peter Parker was sleeping soundly in his crib. Being barely four, he still preferred to sleep in a crib, but Richard and Mary had discussed getting a small bed for him soon.
Of course, Richard wouldn't be there to tuck Peter into his new bed. Or to comfort him, after a nightmare, or to even celebrate the countless birthdays that Peter would have.
Richard deserved nothing less.
He gazed around Peter's room. It was bare, with nothing but the crib, a small closet, and a little desk and chair covered in papers. Peter had only moved into it a few weeks back, and he had always been a neat child. No crayon marks covered the walls, and no toys decorated the floor. His crayons were neatly packed away into their box, and his toys were shut into the closet.
Richard crouched next to Peter's crib and looked down to his face. He brushed aside a stray piece of hair on Peter's face, a tight smile on his face.
"I haven't been the best father, have I?" Richard whispered, resting his hand on Peter's forehead. "I've made mistakes."
He stilled as Peter started to make a few noises in his sleep. Peter quieted down after a few short moments, however, leaving him free to continue his monologue.
"But I'm not the only one who made mistakes. Your mother did as well," Richard murmured. "But it's shameful that it took her mistake to make me realize mine."
Richard stood up, gently taking his hand off Peter's forehead.
"You may not be my son, but I thought you were, all of these years. And that- that, more than anything else, is why I have to leave, no matter how much I want to stay. I have something I need to do. I thought Mary and I would have to leave together, but I can do it without her."
He slowly closed the door to Peter's bedroom, casting one final glance to Peter.
"I have no other choice. I can't trust her, not anymore."
Peter would remember this night. He wouldn't remember much, but what he did remember would taunt him.
After all, he would remember Richard coming to talk to Peter on the day he died, but not what he said.
November 27th, 2000
"Mary? What's this?"
The sound of Peter's childish laughter echoing into May's kitchen marked a harsh contrast with Mary's solemn expression. The two of them were sitting across from each other at the table. May glanced down at the letter that Mary had just put into her hand.
"If you want to tell me something, you can just tell me-"
"-No." Mary shook her head. "This is for Peter. "
"Peter? My dear, I'm afraid you're just making me more confused."
Mary hesitated, before leaning in. "This is for Peter when he turns fifteen. I want to hope that I'll be there for him then… but I'm not that optimistic. Richard… he was involved in some shady things. I don't think that plane crash was an accident. There are some things that Peter needs to know, things that he's not ready for right now. I can't take those secrets to my grave, whenever that may be."
"Mary, you're being ridiculous," May exclaimed. "Why would someone crash an entire plane full of people just to kill Richard? His death… his death was hard for everyone- is still hard for everyone- and I'm not telling you to get over it. I haven't, Ben hasn't, and I'm sure we won't for a while yet. But please, Mary, please, get yourself together. For Peter."
"I won't ask you to believe me." Mary sighed, running a hand through her hair. "But… just in case, keep this letter for Peter. Please. You can do that for me, right?"
May let out a gusty sigh before accepting the letter. She quickly clenched Mary's hands into hers.
"Please, Mary. Drop these ridiculous conspiracy theories," May said softly. "Peter needs you."
Mary gave May a small, clenched smile.
"Believe me, May, if I could, I would."
Peter dashed into the kitchen, jumping into his mother's lap. He gave Mary a big grin.
"Guess what, guess what?" Peter exclaimed.
"What?" Mary smiled back at her child.
"Uncle Ben showed me 'ow to climb a tree!" Peter said excitedly. A leaf floated out of his hair.
"I see," Mary said, stifling a laugh. She ran her hand through his hair absent-mindedly.
How much longer will I be able to stay with him?
The thought ran through her head, unbidden.
Mary's arms snaked around Peter, grasping him tightly. She buried her head into his shoulder.
"Petey, you know Mommy loves you, right?"
Peter blinked, confused at his mother's sudden mood swing.
"Yeah… I love you too!"
"That's great, Petey. That's wonderful." Mary said, clenching to Peter even tighter.
"Mommy… are you awright?" Peter asked, childish innocence etched onto his face.
"Yes, Mommy's fine." Mary let Peter jump out of her lap. "Now, why don't you go play with Uncle Ben some more?"
"Okay!" Peter said cheerfully, racing out of the kitchen.
May gave Mary a worried look.
"Mary, why don't you and Peter stay here for dinner today? You could do with a break." May suggested. She walked over to the fridge and scanned the contents. She frowned. "Oh dear, it looks like we're all out of eggs… and orange juice. Will Peter be happy with water?"
"No, it's fine." Mary smiled. "I'll just go and buy some orange juice and eggs from a store. It'll take twenty minutes, at most. Peter does love his orange juice."
"If you're sure you're up for it." May said doubtfully.
"May, I've been going to work for weeks and nothing's happened. I'll be fine."
Grabbing her coat, Mary strode out of the room.
That would be the last time May saw Mary alive. On the way to the store, Mary would get hit by a car. The culprit would never get caught, and there would be no witnesses.
At the funeral, May would laugh humorlessly at the irony of it all, all while clenching Mary's letter.
August 15th, 2012
Peter's fifteenth birthday.
It was a small affair with his uncle and aunt, some cake, a couple presents… and one yellow-edged letter that was from his long dead mother.