Hydra in the family

Marvel Cinematic Universe Spider-Man (Tom Holland Movies)
Gen
R
Hydra in the family
Summary
Tony Stark had two sons. Now only one. His son James was kidnapped when he was only a year old. 13 years later Tony Stark Ironman. An avenger. And a dad to 16 year old Harley and 8 year old Morgan. He spent years searching for his missing son, only to be told it was a lost cause. There was a very slim chance he was even still alive.But everything changes when a teenage hydra operative is rescued from a lab destroyed by the avengers during a mission. During blood tests they uncover some life changing news.(Title could change lol)
Note
Hi guys! This is my first time posting a fic! :D I hope you like it!!

Chapter 1

There was a slight humming that was steadily getting louder the more he faded into consciousness. Peter took a silent, deep breath as he tried to remember why he was unconscious in the first place. After a quick mental assessment of his body, he registered a slight ringing in his ears and a dull throbbing at the back of his head. What had happened? Where was he? There was a faint but constant tingle in the back of his neck. Never a good sign.

The last thing he could remember was being in target practice in one of the Hydra shooting ranges. He had lifted the gun, aiming for the human shaped target about 100 yards away, but right as his finger curled around the trigger, the wall to his left caved in with a loud bang that was only made worse with his enhanced hearing. He had been knocked to the ground in the explosion, his head throbbing where a chunk of the wall had collided with his skull. He had heard screaming from the hallway and quickly got back to his feet, holding the gun out in front of him.

In the doorway was a big metal robot. At least he thought so until faceplate slid up, revealing a very human man.

“Shit... you guys they have a kid in h-”

The man wasn’t able to finish getting his sentence out to whoever he was talking to before Peter had pulled the trigger.
The man threw his arm up in front of his face, only barely managing to stop the bullet from going straight through his head. The next minute the faceplate was slammed back down and the man was holding his glowing palm out towards Peter.

“Listen kid, I don’t know if you know who we are but we’re the good guys here. We want to help you get out of here, ok? I don’t want to hurt you.”

Peter stayed quiet. He had been with Hydra as long as he could remember, and one of the very first things he was taught was to stay quiet on missions. It was easier that way. No risk of revealing information he shouldn’t share. Exterminate the target and leave. No need for small talk.

“Can you understand me? Do you speak English?” The man tried.

Nothing.

The man sighed, “Ok kid, just come with me, ok? We’re going to get you somewhere safe, alright?”

Peter didn’t move. He was safe. Hydra had been training him his whole life to be able to protect himself and others while keeping them secluded in an underground bunker where no one could find them. Well at least that’s what he had been taught. But now he’s here having a standoff with a man in a metal suit. How did he get here?

Peter opened his mouth slightly, about to demand for the man to tell him who he was and why he had blasted his way in here, when he heard a slight whizzing noise go by his ear. A look to his right showed a man with short blonde hair lowering a bow and backing away. To his left there was an arrow rooted in the wall. The tip flashing red.

“Sorry Tony, we needed to hurry it up. Duck.”

Peter only just had time to see ‘Tony’ drop to the floor before another explosion happened. However, this time Peter didn’t get up. His ears rang and his head pounded. He could taste blood in his mouth. He thought he heard Tony and the archer talking but he couldn’t make out any words. The two of them came to stand over him but before he could do anything his body gave up and his world went black.

*******

What had happened after that explosion? Where was he now? He couldn’t hear anyone near him, so he slowly peeled his eyes open, only to wince when met with a bright light right above his face.

He gave himself a minute to let his eyes adjust before scanning them around the room. He tensed, seeing he was in a lab. There were a bunch of screens showing different tests and graphs on his right, next to a messy countertop covered in beakers and vials and syringes full of who knows what.

Was this another Hydra bunker? When Peter was about 8 years old, he moved from one bunker to the one he was just in. They had started doing experiments on him when he was young. Too young to even fully remember. He was the only one who didn’t immediately die from whatever they had given him. And the more experiments they did the more his power and abilities grew. They moved him to a different bunker; they said as a reward. For being strong enough to withhold the tests they were doing on him.

At the time he thought that meant he was done with the testing and experimenting. That he had somehow succeeded. But it only got worse after that. They pushed his abilities to the max. Seeing how long his enhanced metabolism could go without food, leaving him hungry for a week before he almost died. But he didn’t.

They tested his strength by deploying a bomb that made the ceiling of an old training room collapse on top of him. He managed to lift it enough to escape but for a moment he thought he wouldn’t be able to do it. He thought he was going to die. But he didn’t.

They tested his enhanced healing by doing all sorts of things to his body. Slicing him with knives, stabbing him in vital organs, snapping bones, severing ligaments. He always healed. Normally within hours, but that didn’t mean he didn’t feel the pain. There was one time they broke his left leg, his ankle, sliced a nice sized gash in his forearm and stabbed him in the lower stomach all at the same time, after withholding food for a few days. That time it took him about a week and a half to fully heal every wound, only being given the smallest amount of food possible during the healing process. For a while there he thought he wouldn’t be able to heal himself. He thought he was going to die. But he didn’t.

Sometimes Peter wished one of these tests had killed him. After fourteen years of none stop torture and testing and experimenting and body modification... Sometimes he wished he would die so he wouldn’t have to go through it anymore. But he never did.

Peter shook his head to clear his thoughts. If he thought about it too long, he would send himself into a panic attack and his Hydra handlers always told him that super soldiers didn’t have those. Unfortunately, Peter’s biggest weakness was his own mind. Not in terms of brains. He took pride in being their smartest super soldier to date. Being on par with some of Hydra’s own scientists. But he occasionally let his emotions get the best of him. He’d sometimes get a weird feeling in his stomach before shooting his target, giving them almost enough time to escape before he snapped out of it and carried through. He always got punished for it, but he was told as he trained more and grew older, he would stop feeling things and would eventually be their perfect soldier.

He tried to lift his arms, but they got caught. He was strapped down on a cold metal table, with thick cuffs on his wrists and ankles. He didn’t know what they were made of but even his super strength did nothing on them. Why was he here? We’re they starting new experiments on him? Would they be worse? He struggled for a few minutes before freezing when he heard voices approaching. He went still, closed his eyes and breathed in slow, measured breaths as the door slowly opened.

“He’s still asleep,” A voice said quietly, closing the door behind him with a click.

“Clint’s arrow really did a number on him huh?” A more familiar voice joined, “With all of those enhancements I would have thought he’d be awake by now.”

Peter listened as Tony moved a little closer to the table he was strapped to.

“Some of the files Nat found dated from this week showed that they were withholding food from him to test how his focus fared when running on low energy. That compared with the two explosions he was caught in? Yeah, he’s probably exhausted.”

“What other files did she find?” Tony asked.

Peter heard the other man move closer to him from the other side.

“There’s… there’s a lot. Poor kid’s been through basically every awful thing you could think of. Nat and Sam are compiling and organizing everything they found. Fury wants to be there when we go over everything.”

“Course he does,” Tony scoffed.

Peter heard it before he felt it. Thank his enhanced hearing and his experience with being experimented on. He heard the telltale sound of a syringe be filled and then felt a light jab in his upper arm. It didn’t really hurt, but he didn’t know what he was being injected with. Normally the scientists would tell him what was happening. Sure, it was only to taunt him, knowing he couldn’t stop it no matter how awful it sounded, but at least he still semi knew what was coming.

Before he could fully realize what he was doing, Peter was already in a sitting position, his eyes open wide, doing his best at elbowing away the hand holding the now empty syringe.

“Woahhh,” Tony said, putting his hands up in surrender, coming around the table to stand next to the other man, “Have you been awake this whole time?”

“What was that? What did you inject me with?” Peter asked, ignoring Tony’s question. He tried to seem tough, but his voice wavered from disuse.

“It was nothing to hurt you,” The man said quickly, “It was just some nutrients. Your body needs them, it’ll help you feel better.”

Peter furrowed his eyebrow slightly. Why were they giving him nutrients? Why are they making him feel better?

“Bruce here is a doctor,” Tony said, gesturing to the man who was now sheepishly fixing his glasses.

“Well not-”

“He fixes all of us up after missions,” Tony cut Bruce off, “You got top of the line health care here.”

“Where is here? Where am I?” Peter asked, looking around for a hint.

The room they were in had no windows and he had no recollection of being brought here. It made him uneasy. He curled his hands into fists, being reminded of the cuffs around his wrists.

“You’re in a med lab in Avengers tower,” Bruce stated.

“New York,” Tony supplied, seeing Peter’s confusion.

New York? His bunker was in Sokovia. How is he now laying in a med lab in New York? Why would they need to move him here? What tests did they have lined up next that would need him to move countries?

“We know you’re probably confused and scared-” Bruce started.

“I’m not scared.” Peter cut him off.

Tony raised an eyebrow, “Well good, because you shouldn’t be. We’re not going to hurt you. We’re not like them.”

Peter tilted his head slightly, looking between Tony and Bruce.

“You’re not with them? I’m not here for more testing?” He asked quietly.

Something akin to pity flashed briefly across the two men’s faces. Peter hated it.

“No kid, you’re not. You’re not going to go through that ever again, ok?”

Peter suddenly felt a little lightheaded. His mind couldn’t keep up with everything that he was being told right now. He was in New York, in a med lab, not to be experimented on? The men currently watching him very closely weren’t part of Hydra. They said not to be scared of them, and that he’d never be experimented on like that again.

It sounded too good to be true.

He didn’t believe them.