Hi everyone!

Welcome to my newest story! I thought I would try my hand of Tony being Peter's biological parent and came up with this story!

Firstly I would like to say that I have no idea how kidnapping cases actually work so this is a complete work of fiction and made up by my imagination. I also have no idea how the FBI works so that is also fiction.

Secondly this is set before Homcoming and loosely follows Iron Man and The Avengers time line. I have taken some liberties so please keep that in mind.

I will update the tags as I go along as at the moment I can't think of them all.

Apologies for any mistakes and I hope you all enjoy :)

Summary: AU – Peter Stark was kidnapped when he was just three years old. Tony and Pepper never stopped looking for their boy. Years later, Peter finds his way back home.

Coming Home

Part One

Tony Stark smiled as he felt warm arms slip around his neck, petite hands settling over his heart and arc-reactor.

"What are you looking at?" Pepper hummed in his ear.

"Just viewing the latest YouTube clip of the Spiderling vigilante," Tony said, eyes never leaving the Stark Tablet in his hands.

"What has he done this time?" Pepper asked.

"On today's vigilante swing," Tony tapped at the screen, pressing play on the video. "He rescued a stray dog about to be hit by a car."

Pepper watched as the blue and red figure swung down in the front of a car, the horn blaring loudly, and scooped the dog up with his free arm, just before the car came speeding past. The one they were calling Spider-Man landed lightly on the sidewalk, putting the dog down safely. She watched as the blue and red vigilante patted the dogs head before he was shooting a web at the nearest building and swinging away.

"Amazing," Pepper said softly.

"That tensile strength of that webbing is off the charts," Tony shook his head lightly. "I wonder if they're the manufacturer of it or if they're getting it from somewhere else."

Pepper placed a kiss on her husband's cheek. "You could ask him."

"I'm going to have to," Tony sighed.

"What do you mean?" Pepper asked.

"Fury wants to know who this guy is," Tony said. "He's starting to make a big name for himself and you know Fury, he likes to know everything about everyone. Especially when they are enhanced like the Spiderling appears to be."

"He saved a dog from being hit by a car," Pepper pointed out. "I don't think he's dangerous."

"Fury thinks he could be Avenger material," Tony switched the tablet to sleep mode and settled back into his wife's embrace. "I disagree solely on the onesie he's wearing."

Pepper chuckled. The suit the vigilante was clearly a handmade costume. Whoever the vigilante was, they were obviously on a budget.

"Boss, the FBI are calling," FRIDAY's voice filtered through the workshop.

Pepper frowned, pulling back from Tony's shoulder's, allowing her husband to spin around on her stool. She raised a brow at his confused expression. "What did you do now?"

Tony scoffed. "I didn't do anything. How do I know they're not calling about you?"

Pepper smirked. "Because I would never get caught."

Tony mirrored her smirk, sneaking an arm around her waist. "Patch them through FRIDAY."

"Mr Stark. This is Agent Williamson from the FBI."

Both Pepper and Tony froze as the man introduced himself. The name was one they knew well but had not been one they were expecting to hear from for another few months.

"What can I do for you, Agent Williamson?" Tony asked, arms tightening around his wife's waist, his voice steadily controlled.

"Mr Stark, my apologies for calling so early," Agent Williamson said.

"It's fine," Tony said. "What can I do for you?"

"My office was alerted when a fingerprint was run through our system yesterday," Agent Williamson said, always getting straight to the point. "Mr. Stark, the fingerprint was a match to your sons, Peter Stark."

Pepper's hands flew to her mouth, Tony's tight grip on her waist the only thing keeping her upright. She locked eyes with her husband, watching as the blood drained from his face and his lips became a thin line.

Eleven years ago, while Tony had been kidnapped and trapped in a cave by a group of terrorists for three months, Pepper had been left alone with their three-year-old son Peter. To her horror and devastation, Peter had been taken in the dead of the night. While Rhodey searched for her husband, Pepper and Happy had worked with the FBI to find their son.

Tony had been returned to her, harmed, injured but alive but they had never found Peter. As it came to light that it had been Obadiah who had been the one to orchestrate Tony's kidnapping and Peter's, the man had never given up their son's location before he died. They had poured over Stane's files, but the man hadn't left a trace. That had not stopped Pepper and Tony from using all their available resources into finding their son, including SHEILD but they had never uncovered where he was.

"Are you positive?" Tony managed to choke out.

"We brought in the boy for some questioning last night and to run a blood sample against the one you provided us," Agent Williamson said. "Are you available to come to the FBI?"

"We'll be there in ten," Tony said before he had FRIDAY end the call.

"Peter," Pepper whispered, tears spilling down her cheeks. "Tony."

Tony buried his face in Pepper's stomach, clutching her tightly. He took a few steadying breaths, trying to get his thoughts in order but he couldn't get past the constant stream that they had found his son. Pepper's fingers found their way into his hair, gently brushing through the strands. He shuddered, pulling back and swallowing hard. He stood, gently cupping his wife's face and wiped away her tears. He kissed her forehead before pulling back.

"You get the picture of Peter and I'll get Happy to meet us out the front," Tony said.

Pepper nodded, almost frantically, before she spun on her heels and left the room.

Tony swayed as she left, his heart clenching painfully. He took a few uneven breaths before he ran a hand down his face. "FRIDAY, call Happy and get his ass out the front."

Peter Parker's legs bounced as he took in the small waiting room. He sat in one of the comfy chairs that was provided, leg bouncing as he waited. There was a tall plastic smelling plant in the room and a painting hung on the wall. A table sat across one of the walls, refreshments available if he wished for one.

He didn't, his stomach twisting with nerves.

He and May had been on their way home after eating at their favourite Thai restaurant when they had been stopped at the front of their apartment. By the FBI. They had offered no explanation other than they needed to come down to the FBI to sought something out and if they didn't cooperate, they would be arrested.

Peter's first thought was that they had found out about his alter-ego, Spider-Man. On the car ride there May had tried to get them to answer why they were being detained but they had not said a word. When they arrived, Peter and May had been separated and he hadn't seen his Aunt since.

The door opened to the waiting room and Peter straightened, eyeing the sharply dressed man who entered.

"Peter? I'm Agent Williamson," the man introduced himself with an easy smile. "My apologies for keeping you waiting." He crossed the room, taking a seat near Peter.

"I'm Peter Parker," Peter introduced and then winced. The FBI most likely knew who he was since they had been waiting for him and May. "Where's my Aunt?"

"Your Aunt is answering a few questions for us," Williamson said.

"What kind of questions?" Peter swallowed.

"May Parker is helping us clear up a few things for us," Williamson smiled. "You aren't in any trouble, Peter."

"Oh," Peter blinked. "Okay. That's good. I mean – I hadn't done anything to warrant being in trouble."

"I know you haven't," Williamson said. "Peter, are you up to answering a few questions for me?"

"Um, yes, I guess so," Peter shrugged. "What do you need to know?"

"Great," Williamson smiled. He leaned forward, elbows resting on his knees and his hands clasped together. "How long have you been living with May Parker?"

Peter blinked, brows contracting together. "My aunt? Ummm, since I was six or seven. She and my Uncle Ben took me in when my mum and dad died."

Williamson nodded. "Your uncle passed away recently, didn't he?"

Peter looked down at his hands, watching his fingers twist together. "Yeah, about six months ago. He was – um – he was shot by a mugger."

"You were there?" Williamson asked gently.

Peter nodded; his throat tight. "I – we were coming home. Uncle Ben had taken me out for ice-cream to celebrate an A I got in my chemistry class." He took a shaky breath, his nose starting to sting. "We were just walking home."

"I'm sorry for your loss, Peter," Williamson said.

Peter nodded. "Thank you." He looked back up at the FBI agent. "Umm – the police took my statement months ago. Why are you asking about Ben?"

Williamson didn't answer his question. "What do you remember about your parents?"

Peter frowned. He was beginning to think that maybe this had nothing to do with his alter-ego. "My parents?"

"Richard and Mary Parker," Agent Williamson prompted. "What do you remember about them?"

"I know they were scientists," Peter said slowly. "I don't know what kind though. I remember my dad doing experiments with me. You know, stuff with magnets and dropping Mentos in coke. I – I don't remember a lot about them."

"Did Ben and May ever tell you stories about them?" Williamson asked.

"Uncle Ben was my dad's brother," Peter said. "He would tell me stories about them growing up. Uncle Ben told me about how my dad met my mum at a convention. They would travel a lot for their work. That's how they died. They were heading out on a business trip and their plane crashed."

"And you were staying with May and Ben Parker at the time," Williamson said.

"Agent Williamson? What is this all about?" Peter asked. "Why are you asking me questions about my parents?"

"Peter," Williamson's voice was gentle but controlled. "You had a police officer come to your school today, correct? For careers day?"

Peter blinked at the rapid change in conversation. "Yes."

"And he went through the process of his job," Williamson continued.

Peter nodded.

"He also went through the process of fingerprinting and how each one is unique. He even let your class participate in fingerprinting," Williamson said.

"Were you there too?" Peter blurted out, confounded as to how the agent was detailing the officer's presentation exactly. He didn't remember seeing the agent there at all.

"No," Williamson chuckled. "I spoke with that officer earlier today."

"How come?" Peter asked.

"The officer put your class's prints through our database to demonstrate how we use prints to find a person's identity," Williamson explained. "When he did this, we were sent an alert when your prints showed up in our system."

Peter swallowed. They knew. They knew that he was Spider-Man. Peter was sure that he had always worn his gloves when he was out patrolling but maybe he had slipped up and left his prints at a crime scene. Oh god he was going to be arrested.

"Oh?" Peter squeaked out.

"Peter, what I am about to tell you will be a shock," Williamson said seriously. "But we are here to help you. Okay?"

Peter couldn't speak and stared at the agent, willing his heart to stop racing in his chest. They were going to arrest him. They were going to take away his homemade suit and throw him in jail all because he was trying to help.

"Peter, your prints were in our system because we've been looking for you since you were a baby," Williamson said.

Peter opened his mouth to defend that he wasn't Spider-Man when the Agent's words kicked in. "Wait – looking for me?"

"Peter, Richard and Mary Parker were not your parents," Williamson said. "Your last name isn't Parker."

May Parker straightened as the door to the interrogation room was opened. A female agent, dressed in an expensive looking back pant suit stepped into the room, the door clicking behind her. She looked around the same age as May, blonde hair pulled back into a severe looking ponytail. Strictly business.

"Where is Peter?" May demanded.

"Peter is safe," the agent said, taking a seat on the opposite side of the table. "I'm Agent Harper. I need to ask you some questions about Peter."

"Is he okay?" May swallowed. "Is he in some kind of trouble?"

"He's fine and not in any trouble," Harper said, flipping open a file she had placed on the table. "You are Peter's current guardian, correct?"

May placed her hands on the table, shifting in her seat. "Yes. My husband and I took in our nephew when he was six. His parents were killed in a plane crash."

Harper nodded. "You were not related to Richard or Mary Parker, were you?"

"Only by marriage," May pushed her glasses up her nose. "Ben was Richard's brother."

"Ben passed away recently, correct?" Harper asked.

May swallowed around the tight lump in her throat. "Yes. Six months ago. He was killed in a mugging. Peter was there with him." She inhaled shakily. "The police talked to him about this already. They took his statement."

"I have the report here," Harper tapped the file with her pen.

"Then why did you ask me about it?" May snapped. She took another shaky breath. "What is this all about?"

"You continued to care for Peter, even after your husband's death?" Harper asked, ignoring May's outburst.

"Of course," May huffed. "Peter's family. My family. I would never abandon him."

"Were you there for the birth of Peter?" Harper asked.

May blinked at the left fielded question. "What?"

"Were you present when Mary Parker gave birth to Peter?" Harper repeated.

"I – no. No, neither Ben nor I were there," May hesitated.

Harper nodded, making a note. "When did you first meet, Peter?"

Something churned uncomfortably in May's stomach. "Three. Peter was three years old when Richard and Mary first introduced us to him."

"Why so old?" Harper asked, cocking her head to the side. "Your first and only nephew and you only met him when he was three?"

"Mary and Richard weren't living in Queens," May argued. "They were away on business. Ben and I didn't hear from them much – a phone call once a month was the most contact Ben had."

"How well did you know the Parker's?" Harper asked.

"Not very well," May admitted. "They were always travelling for business and after Ben and I got married they had accepted a job across the country. They came back after three years and that's when we learnt of Peter."

"You didn't question why they hadn't told you about their first-born child?" Harper asked.

"Well, it was a little weird," May agreed. "But Ben and Richard weren't super close. Ben felt he could never live up to Richard's expectations. He was a scientist and Ben wasn't. Once we met Peter, we got swept up in him. He was adorable. Still is."

"Did you often spend time with Peter before his parents were killed?" Harper made another note.

"We would babysit Peter when Mary and Richard were travelling for business," May said. "Ben hoped it would bring him and Richard closer together and we adored Peter, so it was no trouble to us."

"How long would he stay with you?" Harper asked.

"A week at a time, sometimes a little longer," May bit her bottom lip. "What is this all about? Where is Peter?"

"When you were looking after Peter, did Mary or Richard Parker ever give you instructions?" Harper asked.

"Instructions?" May repeated blandly. "Like don't let him eat the Lego pieces?"

Harper cracked a small smile. "No. Like if he was injured, don't take him to the hospital? Did they ever tell you not to take him to certain places?"

"Not to me, no," May shook her head.

"Did they give Ben these instructions?" Harper asked.

May sucked in a breath. "I – I don't know."

Harper caught the stutter and her mouth tightened. "But Ben knew something?"

"Peter has asthma," May swallowed, her voice shaky. "Ben always picked up his inhaler from the same place."

"Where?" Harper demanded.

"Some chemist. I'm – I'm not sure. He always picked up a script before Peter ran out. Since – since Ben died, we haven't needed to get one," May rubbed her chest with a frown. "I'm not sure where Ben got the script from."

Harper scribbled notes quickly. "You never adopted Peter when Mary and Richard passed?"

May shook her head. "We didn't need to. In their will they named us Peter's guardian's." She stared at the agent across the table from her, something twisting sharply in her chest. "You said Peter wasn't in trouble. Am I in trouble?"

"You tell me," Harper said, her voice never losing the tightly controlled sharpness of her tone. "Did you ever question Ben about Peter's parents?"

"I never saw a reason too," May insisted. "Peter was never hurt when we babysat. He was healthy, clean, had new clothes and toys. He had no learning disabilities. The opposite, actually. He's incredibly smart, even when he was young. He was a perfectly happy boy and I had no reason to question anything."

Harper nodded.

"Why are you asking about Mary and Richard?" May asked.

"May, were you aware that Richard and Mary Parker were not Peter's biological parents?"

May stared at Agent Harper for a beat. "What the fuck?"

"Am I to take that as a no?" Harper quirked her brow upwards.

"What do you mean Peter isn't biologically their son?" May demanded.

"Mary Parker never gave birth to Peter," Harper said.

"So, they adopted him?" May asked. "Is that what this is? Is his biological mother asking for him?"

"Peter's parents have been looking for Peter for eleven years," Harper said coolly. "Peter was not adopted by Mary and Richard, he was kidnapped."

May sunk back into her seat, staring wide-eyed at the agent opposite her. She turned over the words in her mind, but she simply couldn't grasp them long enough to understand.

"May, did you have any idea that Peter wasn't Richard and Mary's Parker's son?" Harper asked.

"No," May breathed out, blinking dumbly. "They – they kidnapped Peter?"

"We were alerted when Peter's fingerprints were processed earlier today," Harper said. "The FBI and his parents have been searching for him since he was taken eleven years ago."

May covered her mouth with a shaky hand. "Oh my god."

"Have you ever met a man named Obadiah Stane?" Harper asked.

May shook her head. "No, never. I've never heard of him."

"May, did Ben know about Peter?" Harper asked.

Lowering her hand, May opened her mouth several times before any words came out. "I – I don't know. He never said – never said anything. Oh my god."

Closing the file, Harper got to her feet. "Let me get you some water."

May said nothing as the agent left, her mind reeling. Had she and Ben really been raising someone else's child? All these years and May had unknowingly kept a mother and father from their child. Had Ben known? Before Richard and Mary – those strangers – told Ben the truth before they died? Or had her husband uncovered the truth and kept it to himself?

Harper returned and May shakily accepted the glass of water, taking a few sips.

"Where is Peter?" May asked.

"He's being informed of the situation as we speak," Harper said.

"You're telling him alone?" May cried. "How could you do that to him? Where is he? I want to see him."

"You will shortly," Harper said. "I just have a few more questions."

Peter stared at Agent Williamson; not sure he had heard the man correctly, even with his super hearing. "What?"

"Richard and Mary Parker were not your biological parents," Williamson explained.

"Oh," Peter blinked.

When people asked Peter if he missed his parents, he said he did. It was true, but also not true. Peter didn't remember much of his parents as he had been so young when they had passed away and he remembered they often left on trips. He remembered often staying with Ben and May and never feeling unhappy or scared. He did miss his parents, but mostly he missed the idea of what him and his parents could have been. But May and Ben had raised him, had given him a loving home and he couldn't have been happier.

"I was adopted?" Peter frowned.

"Unfortunately, not," Williamson said. "You were kidnapped from your family."

Peter froze, limbs locking in his seat. "I don't feel kidnapped. May didn't – she wouldn't kidnap me. I'm not even related to her and took me in." You're not related to any of them. "She kept me after Ben died. She didn't have to."

"Take a breath, Peter," Williamson coached. "I know this is a lot to take in."

"A lot to take in?" Peter repeated. "You're telling me that I was kidnapped! That the people that raised me, gave me a home, weren't my family at all!" He sunk back in his seat, crossing his arms and shoved his hands under his armpits. "I want to see May."

"You will, soon," Williamson said. "We just need to ask her some questions."

"She didn't kidnap me," Peter nose stung with tears. "She wouldn't do that. They never wanted kids."

"Who?" Williamson asked.

"May and Ben," Peter sniffed. "I asked them why I didn't have a brother or sister once. They said that I was all they needed. They were never planning on having kids. But they took me in when my par- when they died."

"Okay," Williamson said. "Maybe they didn't know."

"May wouldn't do that," Peter said stubbornly. "She wouldn't."

"That's what we need to get to the bottom of," Williamson said gently.

Peter slumped in his chair as he watched the agent get to his feet.

"I'll be back in a moment," Williamson said. "Can I get you any water?"

Peter shook his head and watched as the agent left the room, leaving Peter all alone with nothing but a tight feeling in his chest and wishing that this had all been about Spider-Man.

Happy reading :)