The Secrets We Keep

Marvel Cinematic Universe The Avengers (Marvel Movies) Spider-Man (Tom Holland Movies) Iron Man (Movies)
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The Secrets We Keep
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Summary
“Who are all these people?” Pepper looked at the crowd forming around them.Tony flashed his million-dollar smile that always made Pepper melt. “Don’t worry about them Pep, it’s just business.”So, Pepper let it go. She shouldn’t have. Pepper's life was perfect. Tony was the perfect husband, gentleman and he made her feel like the luckiest woman alive. It was everything she dreamed of.But she soon finds out Tony's biggest secret. So she hides her biggest secret by running away. Problem is, Tony is not about to let her go.
Note
HiiiiiiiiiiiiI'm a mess and this is just for shits and giggles so let me know your thoughts and if I should continue this
All Chapters Forward

Just Me and You, and Ironman Too

“What do you mean she’s not in the coffee shop?” Tony gritted out. What the fuck did Happy do?

“Sir she must have gone out the other exit.” Happy said into his phone as he looked outside the other entrance Pepper must have slipped through.

“What the FUCK were you doing? I pay you to watch my wife, and she disappears?” Tony yelled into the phone, and pulled his jacket on, and grabbed the keys to his Audi.

“Boss, I’m so sorry-“

“Sorry won’t cut it unless you FIND MY WIFE YOU DUMBASS,” Tony screamed into his phone.

“Sir-“ Tony did not let him finish.

“Call in everyone who can be discrete about this. We need to find her. Someone must have taken her to piss me off. And I’ll kill whoever took her away from me.” Tony snarled.

“But sir, what if she wasn’t kidnapped?”

“What the FUCK are you talking about?!” Tony was pissed that Happy could accuse such a thing.

“Well, it's just, this is a new coffee place, she never goes here. I just, am worried that she planned this.” Happy spoke softly, fear laced in his voice. He was trembling thinking about what his boss would do to him.

“We. Will. Find. Her. She is NOT leaving me.” Tony snapped. “You and I both know, that’s not how marriage works in our world. Until death do us part. There’s no leaving me. I will NEVER let her go.”

Happy shuddered, in fear for himself, but mainly in fear for Pepper. The way Tony was talking reminded him of how he used to be before Pepper. When he was erratic and bloodthirsty. Before Pepper, he was a lot less careful and unpredictable. Pepper had seemed to calm him down, but without her, the old tendencies were back in full force.

Tony was about to start up again at yelling at Happy when there was a knock on his office door.

“Find her before I get down there,” Tony ordered, then promptly hung up the phone. He turned his attention to the door.

“Yes?” He said with hostility.

“It’s Nat.” Pepper’s assistant.

After Tony made Pepper co-CEO of Stark Industries with him, she hired Natasha as her assistant. Originally, she had said her name was Natalie. Turns out, she was working for SHIELD, and her mission was to take down the Stark Empire. Tony was all but ready to kill her at the time, but she proposed a deal that saved her life. She was a trained assassin and could protect Pepper. And, for a reasonable salary, she was willing to lie to the US government, SHIELD, and every other government body interested in the Stark empire and would convince them that Tony was not doing any criminal activity, all while remaining as Pepper’s bodyguard. Turns out, she was incredibly loyal to the Stark family. She was deadly too. When they needed an extra hand dealing with a rival mob, she was always Tony’s go-to. And she was incredibly discrete. Pepper thought Nat was just her assistant. Pepper had no idea Nat could kill someone with her bare hands.

 

“Get in here,” Tony called out, and Nat quickly entered, shutting the door behind her. “You better know where my wife is.”

“Isn’t she out for coffee with Happy?” Nat looked at him and noticed the rage plastered across his face.

“And you just let them go?!” Tony couldn’t hold back his anger.

“You know, I’ve been busy cleaning up some of your messes. Do you remember Stefanos? The guy you killed last week for trying to steal your car? I’ve been busy clearing your DNA from that evidence and getting rid of the body. Pepper is safe with Happy” Nat stated.

“Obviously I don’t remember,” Tony rolled his eyes. “I kill too many people to remember why I killed each one. But the point is, she’s not with Happy.” Tony grunted out.

“What?” Nat asked with shock.

“Turns out, the new coffee shop has a back entrance, and she’s gone. Happy, the terrific bodyguard that he is, had no idea until 15 minutes after she went inside. The dumbass had no idea she was gone.”

Tony looked down at his lap, trying to hold back the tears. He was angry, but mostly, he was worried. What if one of his enemies took her? What if they hurt the love of his life? He would never be able to forgive himself if something happened to her. Did she mean to leave? Or is she lost? Why would she have left him though? They were so happy, and she hadn’t shown any signs of fear after she found out the truth of the Stark mob.

“We will find her,” Nat tried to reassure Tony, “I won’t stop looking for her.”

“Neither will I.”

--

Pepper had never been to Queens. Tony had always referred to it as a dump. He said it had nothing to offer, which is why Pepper had never been there. Despite her fears, it was the only place she could afford. With only 5 grand in her purse and no access to any of her savings, she had to start over. Becoming Mary meant a fresh start, and she had to get used to that. She knew she would have to find a job, something that paid enough to get benefits but not too much to draw any attention to her. No one could find her. No one.

As she stood in her new tiny one-bedroom apartment in Queens, she touched her stomach. Her baby was in there. Hers. And she was determined that she would be able to give him or her a good life. Away from the mob, they would be safe together.

After being here for almost a week, she had started to get some furniture. Used and cheap, it was all she could afford. She missed the plush couch she and Tony had in the penthouse, but she refused to let herself think about it. When she thought about Tony, all she could do was cry. She took a deep breath and went back to decorating her apartment. As she was rearranging her sofa, she heard a knock on the door.

‘Oh god, they didn’t find me, did they?’ Pepper thought worriedly, her heart started beating faster. She looked through the peephole to see a woman and a man she had never seen before. She hesitated on answering it when she noticed they had a loaf of some kind of bread in their hands.

If there’s one thing Pepper noticed about her pregnancy, she was hungry all the time.

She opened the door and looked at the man and woman. The woman had long straight brown hair and had a big smile that reached her eyes. Seeing her smile, made Pepper smile. The man also had brown hair and his smile was just as warm as hers.

“Hi,” Pepper said. “Can I help you?”

“Hi,” The woman started, “My name is May Parker, this is my husband Ben, we live across the hall and wanted to come say hello. We saw you moved in last week.”

“Oh yea I did,” Pepper smiled genuinely, “I’m uh Mary.” It was still weird to say that. “Mary Fitzpatrick.”

“It’s nice to meet you, Mary,” Ben held out his hand, and Pepper shook it. She then shook May’s hand.

“It’s so nice to finally have a young neighbor across the hall. Most of the people that live here are old and boring.” May laughed as she spoke. To Pepper, she seemed like a genuinely happy person.

“Well hopefully that means it’s a quiet building?“ Pepper asked, hoping it would be true. The less social the building was, the less risk there was of anyone in the mob finding her and her baby.

“Ha I wish,” Ben rolled his eyes. “A lot of the old-timers can’t hear their grandchildren on the phone and yell into it. And it’s always at 6 am on a Saturday, who calls their grandchildren at 6 am?”

“That’s actually kind of funny,” Pepper let out a soft laugh. It was soft, but it wasn’t forced.

“Oh, and before we forget, we made you a walnut date loaf.” May held out the dish, and Pepper took it.

“Wow that’s so kind of you, thank you!” Pepper smiled, ready to eat half of it since she was so hungry. “I would invite you in but my place is a mess…” Pepper opened the door fully to reveal the scattered boxes with furniture.

“Oh nonsense. You’re still getting settled. If you want, you should come over for dinner sometime!” May grinned, she was happy to finally have a neighbor around her and her husband’s age.

“Yes, you should!” Ben quickly agreed. May and Ben had the same thought. Mary seemed like a nice woman, and they could use more friends in the building.

“Wow you are both so kind, really thank you. Moving here I was so worried I would be lonely, but now I don’t think I will be.”

“Duh, we will knock on your door and bug you to come over.” May grinned, excited to get to know her new neighbor. Pepper grinned back.

“Where did you move from?” Ben asked.

“Upstate,” Pepper responded. Her birth certificate said she was born in Albany, so it made it easier for her to just stick with that. Small town girl who grew up outside of Albany and dreamed of going to the big city finally made it.

“Where upstate? It’s so beautiful up there.” Ben asked.

“Just outside of Albany.”

“How nice,” May commented. But then her phone rang. “Oh I gotta take this, it’s the hospital. It was so nice meeting you, come over soon okay!”

“Yes, please come over anytime.” Ben smiled softly at her.

“Will do, thank you both.” Pepper smiled and waved, then closed the door.

--
“You find her?” Tony’s head snapped up when he heard the door to his office open.

Rhodey, Tony’s consigliere, shook his head. “No,” he said solemnly.

“FUCK!” Tony slammed his hands on the desk.

“We need to do more,” Rhodey suggested.

“We do,” Tony agreed. But what more could they do?

--

“And you’ll never guess what this guy had stuck up his butt,” May laughed and didn’t wait for Pepper to guess, “An apple!!!! I’m telling you, being a nurse is rewarding, but people sure are weird.”

Pepper laughed and touched her stomach. After a few months, she had really gotten to know the Parkers. They were fantastic neighbors and even better friends. She told them what she could tell them, about how she was starting a new life here in Queens. She even told them that she was expecting. And they were supportive. May excitedly told her about being a nurse at a hospital nearby and promised to make sure she would have one of the less creepy doctors help her deliver. They spent their free time together, just hanging out and watching movies in the Parker apartment. With all the changes in Pepper's life, she was most grateful for the Parkers. She became so close with them after these few months of living in Queens, that she felt like they were her family.

“You know,” Ben broke their fits of giggles, “We aren’t able to have kids.”

Pepper looked at him with raised eyebrows, what was he implying?

“I think what Ben means,” May caught Pepper’s confused look, “is that while we only just started to get to know you, we would be happy to help you and your baby. I’m sure it’s scary knowing you’re bringing a baby into this world alone, but we can support you. We are always here for babysitting.”

“Exactly,” Ben stated. “We want to be a part of your baby’s life; at whatever capacity you feel comfortable with, Mary.”

“Wow,” Pepper started to tear up, overwhelmed by the love she felt, “that means so much to me, thank you.”

“Please, thank you. We always wanted kids, but we couldn’t.” Ben said, with a hint of sadness in his voice.

“Are you going to get maternity leave?” May asked. After Pepper had moved here, she immediately looked for a job. She quickly landed a job as an administrative assistant. Back to square one. It reminded her of her first few days of working for Tony.

“Yea, I get 12 weeks.” Pepper sighed. She knew if she had stayed with Tony, she could have taken all the time in the world to be with her baby. She wouldn’t of had to work ever again. But at what price if her baby had to grow up to become a mobster and kill people?

“Hey, that’s pretty good! Have you thought about what you’re going to about child care?”

“Umm… no” Pepper looked down, suddenly feeling overwhelmed. What was she thinking? She couldn’t raise a baby as a single mother.

“Like we said, we want to help,” May stated. “And we really mean it. You know I work mostly evening into night shifts at the hospital, right? I can watch the baby during the day when you’re back at work.”

“Oh my god, you would do that?”

“Obviously! Anything for my little godson or goddaughter.” May grinned.

“Niece or nephew.” Pepper stated.

“What?” Ben looked puzzled.

“You’re going to be way more than just godparents to the baby. You’re the only family I have. I want you to be Aunt May and Uncle Ben.”

“You mean that?” May started tearing up.

“Of course, I do,” Pepper said, “You’re both going to be so important to him or her.”

May pulled Pepper into a hug, and they both cried. Finally, Pepper felt like she had done something right for her baby. Her baby might never know their real father, but May and Ben would be even better role models.

She just wished the Parkers would be enough for her little family. After she left the Parker apartment and crawled into her bed, Tony was all she could think about. Despite the dangerous man that he was, she missed him like crazy. She could only wonder whether or not he was okay. Was he missing her as much as she missed him? Because she thought, no, she knew she would miss him forever.

--

Tony stumbled into their bedroom in the Penthouse. It had been months. Months. And no leads. Currently, he was hammered and an absolute mess. He had hoped it would help him forget the pain. If anything, it only made it worse. He missed his wife every waking moment. He even missed her in his sleep. How could he have ever taken her for granted? He missed the way she used to kiss his cheek before bed. He missed the way she would curl up into his side. He missed holding her, dancing with her, being with her. He was completely lost without her.

 

Missing her came in waves. Tonight, he was drowning.

 

--

The next morning, Pepper woke up in a cold start. She wrapped the blankets up around her but still shivered. She thought about the only thing she wanted that morning.

Tony.

She imagined being wrapped up in his arms, cozy and safe. She wished she could be tangled up in their silk sheets right now, bodies pressed up against one another. She just wanted him to hold her, to be able to kiss his cheek and feel his goatee tickle her skin. She missed being able to run her fingers through his hair. She missed how in the morning, he would wrap his strong arms around her, and hold her. She thought back to the times when she would try to get up, but he would tighten his grip and mutter for her to stay. Right now, she wished she did.

Suddenly, she felt the baby kick. She sat up, startled. The baby had never kicked before. Feeling the soft thump against her ribs, she cried. At that moment, it really sunk in that she was having a baby.

And she was going to love this kid more than anything.

--
“Wake up Tones,” Rhodey shook his friend’s shoulders.

“Go way,” Tony muttered into his pillow. He was so hungover, all he wanted to do was sleep all day.

“Common man, you gotta wake up, do something productive.” Rhodey was worried about Tony. Tony had become even more ruthless after Pepper disappeared, but when he wasn’t working, he was an absolute disaster. Drinking all the time. Holing himself up in his lab, doing god knows what.

“No.”

“I won’t leave until you’re up.”

“Fuck off,” Tony growled and turned his head into the pillow. Rhodey yanked the sheets off of Tony.

“Common, up up up,” Rhodey pulled Tony up into a sitting position, and Tony sighed.

“Ugh, are you seriously making me get up?” Tony rubbed his aching head. “What are you, my mother?”

“Sometimes it feels like I am,” Rhodey confessed. He paused and looked at his friend “Man this isn’t healthy.”

“You think I don’t know that?” Tony spat out.

“We are all worried about you, Tones.”

“If you were that worried, you would have found my wife by now,” Tony muttered.

“We are trying!” Rhodey raised his voice. “But we’ve all had to babysit you to make sure you don’t kill yourself doing something reckless. Common man, think about it. You could be helping us by at least taking care of yourself.”

“That wouldn’t help find her,” Tony grumbled.

“Well do you have any ideas? You’re the smartest one here, and yet you haven’t used that big brain of yours. We could use more men on the ground looking for her, but you don’t trust anyone. We need more eyes to look all over the place.”

Just then, Tony’s eyes widened.

“That’s it,” Tony spoke.

“Finally, I’ll call more men.” Rhodey went to leave, but Tony stopped him.

“No,” Tony spoke, “we don’t need more people per se, just more intelligence. A way to look by air. Something that can do more than just a man. Something smarter than a man”

“What are you talking about Tones?” Rhodes asked. Tony looked his consigliere dead in the eye.

“Ironman.”

--

Pepper sat in the waiting room of her OBGYN. It was her last appointment before she was expected to give birth. She was insanely nervous. When the doctor called her in, she laid down for the ultrasound.

When her baby showed up on the screen, her heart skipped a beat.

Her baby. She couldn’t wait to hold him or her.

“So, you decided not to find out the sex of the baby?” The doctor asked, not really remembering her file. He saw so many patients in a day he didn’t really have time to remember any of them.

“Yea, I want it to be a surprise,” Pepper spoke sweetly, never taking her eyes off of her baby on the screen.

“Lots of parents are like that for their first time,” the doctor commented. “Do you have names picked out?”

“If it’s a girl, I want to name her Morgan.” Pepper smiled, thinking of her eccentric uncle Morgan. She loved that name for a girl. “If it’s a boy, I think I’m leaning towards Peter.”

“Very well, just be prepared to provide the name at the hospital for the birth certificate. It’s a hassle to go back and get those forms filled out afterward.”

“Okay, thank you, Doc,” Pepper’s smile faded as her baby disappeared from the monitor. The doctor didn’t even warn her that he was stopping the ultrasound, or that he would promptly get up and leave.

“I’ll see you again soon little one,” Pepper muttered to her baby, who kicked back.

--
“Alright, this is what, test number 112?” Tony spoke out. He was in his lab, surrounded by the armor he had been working on for the past few months. It was now mid-July, and he was getting impatient. He was so close.

“Yes sir,” Friday spoke.

“Alright, commencing test number 112.” Tony stood back, and the armor wrapped around him.

He moved his arms and legs around. Success.

He tested the lasers, the repulsors, the missiles, the minigun. Success.

He put his hands down and propelled himself in the air to fly. Success.

His bots fired a round of bullets at his chest. He looked down and saw no damage. Success.

He stepped out of the armor seamlessly. Success.

He turned on the remote operator and tested all the same functions. Success.

 

Tony grinned. Ironman was born.

 

--

On August 10th, Pepper went into the hospital as Mary Fitzpatrick and gave birth to a baby boy.

She held her baby, and she knew she did the right thing all along. This pain and suffering from leaving her husband was worth it for this small, delicate, and beautiful little boy.

He was perfect. He had tufts of light brown hair that stuck out in every direction and curled on the end. His small fists were bunched up into the blanket Pepper had carefully wrapped around her baby. As he slept, he puffed out these small yet deep little baby huffs of air. And most notably, he was the spitting image of Tony.

“Peter Benjamin,” Pepper whispered to her sleeping baby, “I love you more than words could ever say.”

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