So here is part 2.
I want to make something clear, I am not shipping Peter and Matt as Peter is a minor in this story, just to be clear. I was more going for the little brother, big brother relationship :)

Around 1:24 am, Matt heard Peter fall asleep. 
Around 1:30 am, Matt was sitting at his dining table and searching Peter Parker online, but could not find anything. Like this boy doesn't even exist. Weird. 
Around 2:15 am, Matt stopped searching and went to sleep.
Around 3:43 am, Matt woke up to sounds coming out of his bedroom, whimpers and crying. Is Peter okay?.... Most definitely not.

Matt quietly entered his bedroom to find Peter asleep but trashing in bed. He is having a nightmare. 

"Please... no May... Stop... don't-don't leave me... Help..." Peter murmured. Definitely a nightmare. Matt was thinking about the best way to wake the poor kid up. Not having experience with helping someone with their nightmares. 

Matt walked to Peter, crouching down next to the bed and carefully went to put a hand on Peter. Wrong move. Peter's eyes shot open in panic as he went to punch the person who touched him, luckily Matt dodged, but that didn't help with Peter's panic. A hyperventilating Peter was now on the other side of the bed, staring at Matt with wide eyes. 

"Hey, it's okay. It's just me, Matt." Matt said softly as he raised his hands like he was surrendering. Peter's breathing started to slow, he swallowed hard before talking. 

"Sor-sorry for waking you up," Peter whispered. 

"No. You don't have to be sorry. It's okay." It's not, this kid shouldn't go through all of this. 

There was a short period of silence where Peter calmed down. 

"Do you want to talk about it?" Matt asked.

"I- uhm... You don't want to hea-" 

"I don't mind, I promise." 

"Oh uhm, yeah okay... But like, you don't have to sit on the floor, I feel bad enough that I sleep in your bed but please don't sit on the floor now." Peter almost begged Matt to stand up.

"Yeah okay, you okay with me sitting on the bed?" Matt asked, not wanting to do something the kid wouldn't like. Peter nodded, too tired to remember Matt was blind. When Matt was still staring in Peter's direction Peter remembered. 

"Oh uhh, sorry. I don't mind." 

"You nodded, didn't you?" Matt chuckled. 

"Yeah, I did." Peter chuckled too, lighting up the mood a little. There was a short period of silence again where Matt moved onto the bed and sat with his back against the wall.

"So uhm... yeah... It's hard to start, cause so many things happened. And I don't- I..." Peter sighed loudly, frustrated he could not find his words. 

"Hey, take your time. You don't have to rush this. Take your time to find your words." 

"Thanks," Peter muttered. He stared out the window for a sec before continuing.
"5 months ago my life turned around for the second time. And it sucks. My uhm... nightmares were multiple things, multiple traumatic events I've been through. 5 months ago, my aunt was killed by a bad guy. My last living relative, the person who had been feeding me, giving me clothes, and helping me with homework, died because of me... The person who raised me since I was 5... died... And not that long before that my mentor, and actually kinda my father figure had also passed away. It's like everyone I love dies..." Peter was full-on crying right now, and Matt was doing his best not to. To make the story even sadder, it also started to rain outside.

This kid needs a hug. And Matt was right, when he opened his arms Peter hesitated a second before diving into the hug. Something he needed. Matt rubbed Peter's back, trying to comfort the crying teen. Eventually, Peter fell asleep again, in the safe arms of Matt. 

8.30 am (Matt somehow escaped Peter's grip)

"Foggy I need some help." 

"What do you mean Matt? Everything okay with that spider guy?"

"No, he told me his name and I tried to search for him online, but nothing. Could not find anything, no school report, no family or anything." 

"Oh damn. Did he give you his real name?"

"Yes, he did not lie. Everything he told me was the truth. And he told me a lot."

"But why do you need my help?"

"He's a kid, Foggy, a kid! And from what he told me he has been through way too much for someone his age!" It angers Matt to think about what the kid has been through, and he knew Peter hasn't told him everything yet. 

"Oh, shit. Want me to come over later? Figure this out together?"

"I don't know. I don't want to scare him."

"Understandable."

"You know what scares me?"

"What?"

"He knew who I was when he saw me without the mask. And I'm pretty sure when I asked why he wanted to say that I represented him as a lawyer. I remember every client I helped, and I did not help him."

"What about it scares you? Maybe he just lied about it."

"That's the scary part. He did not lie about that either."

"Weird, very weird. You sure you did not help him or anyth-"

"I got to go, he's waking up. I will call you later." Before Foggy could even respond Matt hung up the phone. Leaving a worried Foggy. 

Matt leaned against the wall, thinking about what the hell he should do. He heard footsteps coming his way so he grabbed his glasses and went to the kitchen, hearing the kid's stomach rumble. 

"Morning Peter. How did you sleep?" 

"Uhh, honestly, even after waking up in the middle of the night, this was the best and longest sleep I've had in a while," Peter answered, yawning a bit while doing so. 

"That's nice. How's the wound doing?" Matt asked while grabbing some eggs and bacon out of his fridge. 

"Uhh yeah, still healing but it doesn't hurt as much anymore." Peter lied, he was in terrible pain, and he hoped Matt would not notice him lying. 

"Pete, don't lie to me, I can hear your heartbeat. And I can also hear you grunt silently in pain." Matt looked in Peter's direction with a serious face. All Peter did in response was a small oh sound. 

"It's still raining cats and dogs," Peter said to change the subject. Smooth Pete. 

"It is, they say there is also going to be thunder and lightning later the day." 

"Wonder who pissed off Thor." Peter laughed, stopping quickly as it hurts a lot. 

Peter sat down at Matt's dinner table and observed how Matt was cooking, remembering watching May like this made him smile a bit. Good memories. After 5 quiet minutes, Matt brought 2 plates with food to the table. 

"I hope you like eggs, bacon and toast. That was the only thing I had in my fridge." Matt said kindly. Setting a full plate in front of Peter. 

"Matt, you didn't need to make all this. I'm not that hungry!" Another lie, but Peter felt guilty about this, not wanting to rob this man of all his food. 

"I don't mind. And I could hear your stomach rumble and figured you needed some good food." 

"Thanks." Peter inhaled his food as he really was hungry. Finally, enough food to settle his stomach he immediately felt better. Closing his eyes as he felt his wound slowly closing. 

There was knocking on the door which scared Peter. 

"Who's there, you didn't tell anyone else about me, did you? I hope you didn't cause I don't like that. Please tell me you did not, please." Peter was talking really fast as he was starting to panic a little. 

"Peter calm down. It's Foggy, my friend. You can go to my room if you want to." Matt tried to calm him down, not answering the question Peter asked. But Peter didn't seem to notice as he just nodded fastly and almost sprinted to Matt's bedroom. 

Peter was not listening to the conversation in the living room. He was too focused to try to not go into a full-blown panic attack. Sitting on the bed hugging his knees and focusing on his breaths, how Mr Stark learned him. Something that did not help was that it started to thunder outside. Bright lightning and loud thunder were not helping. Closing his eyes and clamping his hands over his ears trying to block it all out. Sadly it was barely helping. 

Soon he could feel everything, how the shirt was sitting on his body, how the bandage was wrapped around his waist. Everything started to irritate, getting itchy and burning. The bright flashes from outside were painful for his eyes, even through his closed eyes. The thunder was too loud, everything was loud. He could smell what had been eaten in almost the whole building.  Where someone was showering, some couple was arguing. It was all so loud and painful. Gasping in pain hoping it would be over soon. 

5 minutes back

"Foggy, what are you doing here?" Matt asked as he opened the door. 

"I could not let you handle this alone, I'm your partner." 

"Yes, I know. But I told you I didn't want to scare the kid. And you just kinda did." 

"What do you mean?"

"He panicked when you knocked. But he is calming down, I can hear." 

"Oh, okay. Sorry, I didn't mean to." Foggy felt guilty, he meant to help the kid, not scare him. 

They stood there in silence when a loud thunderclap sounded. Making Matt wince from the loudness. 

"I'm never going to get used to that," Matt said quietly as he walked back into his apartment, Foggy following.

"How do you experience it?" Foggy asked curiously. 

"Well, it's like a gun being shot right next to me, very loud and all."

"Oh, that must suck."

"Yeah." And yet again, silence. Matt listened to the kid, trying to hear how Peter was doing. 

"Shit!" Matt exclaimed as he stood up in a rush. Remembering something the kid told him yesterday about his enhanced senses and about getting into sensory overloads a lot so he would always have a pair of noise-cancelling headphones. Finding the spider suit was one thing, but trying to figure out how these pockets worked was another. Matt just ripped open the pocket to find the headphones. 

Foggy just stood there, figuring out what Matt was doing, but keeping his mouth shut as Matt sprinted to his bedroom with some kind of headphones. 

Peter was sitting on the bed, rocking back and forth, crying with his hand over his ears and his eyes closed. Matt could hear how much pain Peter was in. Matt walked closer and Peter winced with every step Matt took. Peter felt hands on his hands, not wanting to let go of his ears but the other hand were stronger. But soon Peter was embraced with pure silence. Relaxing immediately, he leaned more into the touch as he was exhausted. 

Matt was breathing hard, fighting the kid to get his hands out of the way of his ears was hard, that kid is strong! But eventually, he succeeded and put the headphones in Peter's ears, seeing the kid relax immediately made Matt relax himself. Peter leaned more into Matt yawning. Matt shifted so he was sitting more comfortably. Thinking to himself, This kid really needs some more human touch.

"What happened?" Foggy whispered as he stood at the door opening seeing a kid in Matt's arms. 

"Sensory overload, I think because of the storm. He's exhausted."

"Poor kid, call me if you need anything." Foggy left Matt and Peter alone. Feeling sorry for the kid. 

I will probably write a part 3 since this was getting too long lol.