Chapter 2: SHIELD

Phil Coulson and his team were still reeling from the fallout Hydra had left behind in their wake. Fitz had been seriously hurt by someone they had all trusted. The sting of Ward's betrayal wasn't something that any of them would soon forget.

They had been laying low for the past few weeks, and had only just settled into their new, Hydra free, base. Slowly but surely they had been picking up the pieces. SHIELD agents who were still alive and loyal to SHIELD were slowly trickling into the secure base they set themselves up in.

Phil was still trying to find his footing in this new version of SHIELD that had to work in the shadows with very limited resources. He was doing the best that he could to rebuild SHIELD from the shambles it was in. He didn't know where he would be without his team. He couldn't have been more proud of the way they were holding up. They'd stuck together and somehow they were all getting through this.

Phil was currently in his new office. There were a lot of things that he needed to go over from the cube Fury had given him. There was also the disturbing problem of what he'd been drawing on the wall.

"Hello, Director."

Phil turned.

He had to say he was only mildly surprised to see Natasha Romanoff standing behind him. If any of the Avengers were going to find out he was still alive it would have been Natasha.

She was in civilian clothing but still looked as deadly as ever. She didn't appear to be upset at seeing him alive. Of course sometimes it was even difficult for him to measure what she was feeling. He liked to think he could read her fairly well, and if he was reading it correctly she looked a little tense.

"Natasha, it's nice to see you. How are you?" Phil stood to greet her.

"I think I should be asking you that, considering you're the one that's supposed to be dead," she said casually.

"Technically I was, I just didn't stay that way," Phil smiled as if everything he had suffered and was still suffering wasn't a big deal.

"Right, TAHITI. That's one project that was kept out of SHIELD's main database," Natasha trailed her fingers along his desk.

"Right, I saw what you did with SHIELD's files. All of SHIELD's dirty little secrets out in the open for everyone and their mother to see," Phil had scanned through it to see if his resurrection had been leaked along with everything else.

"Of course, not everything was leaked," Natasha nodded, easily following his train of thought.

"I'm aware. There were some things that Fury didn't trust being put in the mainframe. It's why he had this," Phil pulled out the cube.

"Fury's paranoia has finally paid off. How much have you gotten through?" Natasha didn't even bat an eye at it.

If she knew about him being alive, of course she would know about the cube.

"Not nearly as much as I would like. I haven't exactly had the time what with re-building SHIELD," Phil sighed, suddenly feeling just how exhausted he truly was. There hadn't been a lot of time for sleep lately, and when he did sleep... It wasn't exactly restful.

"There's something I'd like to show you," she looked at the cube expectantly.

Phil understood, and did what she was silently asking. He opened the box and the files sprang up.

Natasha competently navigated her way through the files. She chose one and enlarged it. The rest of the files disappeared leaving only the one behind, floating in front of them.

Phil moved forward to stand beside her to get a better look. He would admit that he was a little surprised to find himself looking at a picture of a little boy with reddish brown curls and blue-gray eyes. The name at the top of the picture shocked him even more. It certainly wasn't something he had been expecting to ever see.

"What am I looking at, Natasha?" Phil asked softly.

The name at the top of the picture read: Romanov, Petrov.

"My son," she answered her voice just as soft.

She waved her hands and the file expanded. Reports, and pictures all pertaining to Petrov Yakov Romanov surrounded them.

"I'd just turned eighteen when I had him. They let me keep him or at least they let me be around him. When he was five I tried to smuggle him out of Russia. I was unsuccessful, and they took him from me. I believed they killed him to punish me for disobeying. It was only 37 years later when a pair of SHIELD agents found him in a cryotube that I learned otherwise. They thawed him out, and the SHIELD agents that found him, Richard and Mary Parker, adopted him. Only Richard, Mary, Fury, Clint, and I knew who he was.

"Richard and Mary died on a mission. Custody was turned over to Richard's brother and his wife at my insistence. Ben Parker died trying to stop a robbery a few months ago but my son still lives with his wife, May Parker. They're great people. I couldn't have asked for anyone better to raise him, to give him a normal life. I've checked in on him now and again. He goes to a high school geared towards science. He's a genius, the second in his class."

Phil would have never imagined he would hear the Black Widow gushing like a proud soccer mom. Phil didn't know whether to laugh or be completely terrified.

He settled for just remaining silent.

"His name is Peter Parker now. He'll be seventeen soon," Natasha brought up a picture from the file.

It was the same boy from the previous picture but more recent, most likely from a school photo. He was older, in his teens now. He was a handsome kid with messy reddish brown hair, blue-gray eyes, and a large grin stretched across his face. Phil could easily see Natasha in his features, and he wondered who the boy's father was.

Natasha was staring at the picture with a deep fondness, love shining in her green eyes.

"What do you need me to do, Natasha?" Phil asked.

"I need you to keep an eye on him for a little while," Natasha stated.

"All right. Why?"

"His identity as my son wasn't on the SHIELD database. Unfortunately, the part about finding a child in a cryotype in an old Soviet bunker was. Richard and Mary's names were on those reports. It's only a matter of time before someone connects them to Peter Parker, and Peter Parker to the little boy in those reports."

"You think Hydra will go after him?" Phil questioned.

"I think it's a possibility. There was information about the Red Room experimenting on Peter in the public files. Hydra will eventually want to know more about their methods. If they don't know already. There's a connection between Hydra and the Red Room. I'm not sure how deeply it goes just yet. It's only recently that I've noticed they had some members in common," Natasha explained her tone clipped, her eyes furious.

"I see," Phil nodded. He made a mental note to look into it himself. When he had the time of course.

He was already trying to figure out who he could spare to watch Peter Parker. However, he couldn't deny the desire to go out and meet the boy for himself. Natasha's son was bound to be an interesting kid.

"Clint's still on his well deserved leave with his family, and there isn't anyone else I trust to do this. I would do it myself but unfortunately I'm still tied up in court with the Senate," annoyance flickered across her features. "So if you can keep an eye on him until I'm free I would be very grateful."

"Of course, consider it done, Natasha," Phil promised.

"Thank you, Phil. It was really nice seeing you," Natasha smiled warmly at him.

"You too, Natasha," Phil smiled back.

Then as quietly as she had arrived, Natasha slipped away.

Phil took a moment to study the rest of the file. It was such a strange concept to think Natasha had a son out there. It was less strange to see that she had allowed him to be raised by someone else.

She would have wanted to give him the life she never had, and she wouldn't have trusted herself to do that. Phil felt a pang at the thought of Natasha watching her son grow up from the sidelines, believing that all of the things she had been forced to do in her past meant that she wasn't good enough to raise her son.

For that reason and because Natasha was his friend he would personally make sure her son was safe. He would fly out personally to scout the area, and send out some feelers to see if anyone was interested in picking Peter up. If everything was all clear he'd leave one of his best to keep a close eye on Peter until Natasha was free.

Phil decided to take the ones he trusted the most on this mission. He left the base to Agent Hartley and her crew. Skye, Melinda, and Trip would be joining him on his trip out to Queens.

The only ones missing were FitzSimmons. But what Simmons was doing was a necessary evil, unfortunately. He just hoped it was the right thing to do. He hated having her there, and didn't want the experience to change her. Or change her more than she already had. They had all been changed by the fall of SHIELD, and he was certain there would be a lot more to come before they managed to defeat Hydra. Fitz, on the other hand, wasn't quite ready for fieldwork. He was still recovering. However, his progress wasn't as swift as they had all hoped especially with Simmons gone.

Phil didn't tell them exactly why they were going. They knew only what was on the public SHIELD database. Peter Parker was just a possible powered person who they needed to check out before Hydra did. As soon as they got to New York City they located Peter through the information provided in the cube.

The mission was supposed to be completely hands off, just observation to make sure Peter was safe. However, it didn't take them long to notice Hydra agents lurking around. Hydra had discovered Peter, and it appeared they were planning on taking Peter in. As soon as they spotted the Hydra agents closing in around Peter they quickly altered their plans. Phil left a quick message for Natasha about the change of plans then he focused completely on getting her son out of there.

Melinda was waiting in the quinjet, Skye and Trip were waiting close by in the SUV to drive them to the quinjet, and he was going to collect Peter. Hydra was planning on grabbing Peter as soon as he reached his home in Queens. They had a trap laying in wait for him there. There were still a few Hydra agents keeping an eye on him now to make certain he was going home.

Phil was going to have to convince him to go with him before he could get there, and before the Hydra agents realized who he was. Phil waited patiently as the students from Midtown High streamed out of the building. It was easy to spot the tall, lean form of Natasha's son.

Phil quickly moved to fall into step beside him, and for a moment he forgot what he was supposed to be doing. It was one thing to see a picture another to see him in person. Peter looked so much like Natasha.

Phil stared too long. It had gotten to the point where it had become creepy. So Peter spoke up.

/

One month had passed since Peter had found out he was technically a 52-year-old Russian experiment.

He'd continued going out at night as Spider-Man. Just because SHIELD was in pieces, and Hydra was running around plotting nefarious Nazi plots it didn't mean that there still weren't run of the mill lowlifes making life difficult for the everyday citizen. It was actually nice since Peter didn't have to worry about J. Jonah Jameson and the Daily Bugle making up some outlandish story about him. They were still too focused on printing stories about the event in DC.

He still kept a close eye on his surroundings. Peter wasn't quite ready to relax his guard just yet. The government was going through all of the SHIELD information. They desperately wanted to be seen doing something in the wake of the devastation caused by SHIELD. Even if it meant arresting members of SHIELD that hadn't been involved with Hydra. It was very likely that they might seek him out for questioning at the very least. Peter still had no idea what he would do if it happened.

But now that he knew his dreams were actually memories, he started focusing on them a little more. Peter was fairly certain he'd gotten nearly all of them back now. At least most of his memories were about his mother, and on the plus side he could now fully speak Russian. Sometimes without even realizing he was doing it. He'd also remembered that he hadn't always been Peter. His first name had once been Petrov.

Peter knew he had only been kept in the lab for a short while before being frozen. It had been difficult to come to terms with the fact that he had actually been experimented on. But both Gwen and Aunt May had been a huge help. He'd talked to them about everything he remembered from the labs, and they'd worked through it. Peter didn't have nightmares nearly as often as he did just a month prior.

It gave him time to think more about where he came from. When he looked up the Red Room on the leaked SHIELD files it turned out that it was the same place that created the Black Widow ops, which was a group of 28-orphaned girls who'd been trained to be assassins and spies.

Peter wondered if his mother had been one of those 28 girls. Either way she was probably gone now either from old age or she had been killed in her line of work. Or she could have even been in hiding to protect herself from past enemies. An assassin was bound to have acquired quite a few over the years. Either way Peter wasn't going to be able to find her anytime soon. He was curious if someone in SHIELD would know her identity. There was a lot of information that had been redacted from Richard and Mary's initial report of finding him. Peter wanted to just what that information could be.

Peter put finding his mother on the backburner. It wasn't something that he was going to be able to accomplish anytime soon. He tried to focus on school and crime fighting. Flash was still annoying, but only because now he was the president of Spider-Man's fan club. Gwen was the best girlfriend he could have asked for. He could always count on her to talk about anything. And he was doing well in all of his classes. There was only one month of school left, and Peter was determined to leave junior year off on a good note after he nearly helped to destroy the school.

Gwen and Peter always said their goodbyes in the school courtyard on the days that Gwen had to go to OsCorp. They made plans for tomorrow, and Peter leisurely started to make his way home.

There was a change to his normal routine. The moment he stepped off of campus a man in a black suit fell into step beside him.

Peter immediately tensed and glanced at the man out of the corner of his eye. He was an ordinary looking man. Not tall or short. His face would have been completely forgettable in a crowd. His light brown hair was thinning at the forehead, and he wore a jovial if bland expression. He didn't appear to be threatening he just walked beside him as if they knew one another, and were walking home together. The man made no moves to grab him, and Peter's spidey sense remained quiet at the back of his skull despite the fact that he was staring intently at Peter.

"So there a reason you're walking right next to me when there's plenty of room on the street?" Peter spoke after a couple of minutes of silence.

"You're in danger," the man stated abruptly, keeping his eyes completely focused in front of him.

"Is that a threat?" Peter demanded, tensing and preparing to fight if he needed to.

"No, it's a fact. See the man reading on the bench?"

Peter turned to look.

"No, don't turn your head. Just look out of the corner of your eyes," the man commanded.

Peter did as he said. The man on the bench was sitting there just calmly reading the paper.

"Yeah, what about him?" Peter asked.

"He's Hydra," the man stated calmly.

"What?" Peter felt panic claw at him.

"I know this might be difficult but I need you to remain calm, and not show any outward signs of distress. Can you do that for me, Peter?" the man asked.

"How do you know my name?" Peter took a few deep breaths and focused on keeping up a relaxed and normal expression.

"My name is Agent Coulson. I don't have a lot of time to explain. I work for SHIELD or well the non-Hydra part of SHIELD. I was sent to watch over you. Your parents were SHIELD agents. But now that Hydra is moving in with the intent to capture you our plans have changed. We need to extract you and move you to a safe location as swiftly as possible," Agent Coulson explained.

"How do I know I can trust you? How do I know you're not actually Hydra, and that if I go with you I won't be walking right into a trap?" Peter demanded.

"Because in a minute the man on the bench will have finished alerting his companions to my presence beside you. In another four minutes Hydra will be descending upon us with the intent of taking you with them. You have three minutes Peter to decide whether or not you can trust me," Agent Coulson said calmly.

"Give me a reason to trust you," Peter demanded desperately.

Peter had no idea what to do if a group of Hydra agents came after him. It would be different if he was wearing his suit. But they would be coming after Peter Parker not Spider-Man. Using his powers would reveal who he was, and they would just come after him with a greater ferocity.

If they didn't know already. Hydra and this Agent Coulson seemed to have made the connection between him and the boy in the cyrotube. What else could they possibly know about him to have decided he was important enough to warrant a kidnapping?

"Right now I can only give you my word that you can trust me," Agent Coulson replied.

This was all happening too quickly. Peter didn't know what to do. But for some strange reason his gut was telling him that he could he trust Agent Coulson.

"Fine, okay. What do we do?" Peter asked, mentally preparing himself for whatever was about to next.

Agent Coulson gave some sort of signal, and a large black SUV pulled up alongside them. Agent Coulson trotted to the side of the car, he pulled the door open, and climbed inside. He left the door open for Peter to follow him in. Peter hesitated for a moment. Was he really about to willingly jump into an unmarked car with a random man who walked up to him on the street?

His hesitation ended when a black hummer squealed around the corner gunning directly for them. Peter's spidey sense went off just before a man in all black gear leaned out of the window and fired at him. He was able to dodge out of the way just in time to see a large silver tranquilizer dart smash into the sidewalk beside him.

After that Peter didn't hesitate to lunge into the waiting SUV. As soon as he was in the driver peeled out of there. Another black armored hummer had appeared around the opposite corner, and was quickly gaining on them from behind. Peter turned to see that another man in black was leaning out of this hummer. But he wasn't firing tranquilizer darts at them.

Peter ducked down as the bullets struck the back windows.

"Don't worry, the windows are all bullet proof," Agent Coulson assured him without a care in the world as if they weren't in the process of being shot at while in a high-speed car chase.

"Well, that's great to know after we've already been shot at," Peter grumbled.

"Should we return fire, sir?" the driver asked.

He was African American with hair cut close to scalp, sharp dark eyes, and a neatly trimmed beard. He looked to be in his twenties, and was a pretty decent getaway driver. He was weaving in and out of traffic at speeds he really probably shouldn't be.

"Not yet, just focus on losing Hydra, and getting us to the quinjet," Agent Coulson replied, keeping an eye on the progress of the two hummers behind them.

"Will do," the driver agreed amicably.

"Skye, how close are we?" Agent Coulson asked the girl in the passenger seat.

She had some sort of scanner in her lap.

"We're about two minutes out from the quinjet," Skye answered.

"Are there any more Hydra reinforcements on their way?" Agent Coulson questioned.

"It looks like there's just the two hummers on our tail. The group watching the house is on their way but we should reach the quinjet before they have a chance to reach us," Skye explained.

"Good," Agent Coulson nodded in satisfaction.

Peter watched as the hummers fell further back, and the shooting stopped. The SUV was big but it was definitely more agile than the hummers.

"So you're really SHIELD?" Peter asked.

"Yup, we're the real deal," Skye turned around to smile at him.

She was pretty with long dark hair, and dark eyes with a hint of Asian ancestry to her features. She looked to be somewhere in her early twenties.

"Okay, cool, at least the whole getting into cars with strangers thing didn't backfire on me," Peter gave a nervous chuckle.

She laughed. "Definitely no worries here. AC here is doing everything he can to put SHIELD back together. Trip here is the grandson of a Howling Commando—"

"No way," Peter breathed in excitement, trying to get a better look at their getaway driver.

"Yup," Trip chuckled.

"We can have formal introductions later. I believe our stop is here," Agent Coulson pointed out.

Trip whipped the car into a sharp turn. The tires squealed as they swung into an abandoned parking lot. To Peter's ever growing surprise there was a jet casually parked there.

"Everybody out, Hydra's still not be far behind and I would prefer to be in the air before they get here."

Agent Coulson didn't need to say it twice. They were all out and running towards the jet before he'd finished speaking. The jet door dropped opened and they quickly made their way on board. The door was still closing as they were lifting off. Peter caught a glimpse of Hydra speeding into the parking lot before the door shut completely. The sounds of gunfire ricocheting off the side of the jet followed them into the air.

It was only when they had reached the clouds that everyone visibly calmed down.

"So what happens now?" Peter asked quietly.

Now that he had a moment to think, the consequences of his situation hit him and hit him hard.

"You're going to come back with us to our base," Agent Coulson stated, regarding him shrewdly. "You don't exactly look too shaken up by all of this."

"Oh, you want me to start screaming? Because I can do that. I'm pretty sure I'm about one second away from losing my sh-ugar," Peter ended lamely. Aunt May wouldn't be pleased if she heard him cursing even if the situation might have warranted it.

"What I mean, Peter, is that you have some understanding as to why Hydra might be after you," Agent Coulson explained.

"I've read the files SHIELD made public. It wasn't too hard to connect the dots," Peter muttered with a shrug.

Agent Coulson didn't look at all surprised by this information. The other two agents looked slightly confused but were trying not to show it.

"Then you understand perfectly why you need to come with us. Hydra doesn't give up once they've settled on a course of action," Agent Coulson regarded him closely.

"I understand, but it doesn't mean I like it. What about my aunt?" Peter panicked as he suddenly remembered Aunt May was still at work. "Hydra could go after her to get to me."

"That's not going to happen. They only want you, and now that they realize we've taken you they won't go after her. They know she isn't aware of your location and she holds no further use to them, and they won't want to waste resources when they're already stretched thin after this failed attempt. However, I will assign someone to keep an eye on her, if you'd like," Agent Coulson promise.

"Yeah, that would be good," Peter nodded fervently. "But I have to call her. To let her know I'm all right."

"We'll find a way to let her know you're alright, quietly. We don't want to bring unnecessary attention to her. Hydra will be monitoring her closely to see if you contact her. If you do they will most likely move in to interrogate her," Agent Coulson cautioned.

Peter nodded reluctantly. He didn't like it, but it made sense. If he contacted her, Hydra would think she knew where he was. They would hurt her to get to him because that's just the kinds of evil, sons of biscuit eaters they were.

"Right, okay," Peter nodded.

He thought about Gwen but he figured the same thing that applied to Aunt May would apply to her. Peter still felt guilty about leaving them to worry over what had happened to him.

"Everything will turn out alright, Peter," Agent Coulson flashed him a small smile.

The man was so calm and steady in all this craziness that Peter couldn't help but believe him.

"Whatever you say, Secret Agent Man," Peter smirked, pulling on some of his confidence he had when he was Spider-Man.

Trip snorted.

"Peter, allow me to introduce Agent Antoine Triplett," Agent Coulson nodded towards the other man.

"Call me, Trip," he insisted as he held out a hand to Peter, a large smile on his face.

"Nice to meet you," Peter shook his hand.

"And this is Agent Skye," Agent Coulson pointed at the young woman.

"Hey," she gave him a little wave.

"Hello," Peter waved back.

"And that's our pilot, Agent Melinda May," Agent Coulson pointed another woman in the cockpit.

She turned briefly to give him a quick yet thorough once over that left Peter like she could see straight into his soul. She was Chinese with shoulder length straight dark hair, and piercing eyes.

Agent May gave him a single nod before turning her attention back to the controls. Peter sensed she was more like Agent Coulson. She'd been in the game a lot longer than Skye and Trip. It was easy to guess that she'd seen and done quite a lot in her time as an agent of SHIELD.

"So how much of SHIELD is actually left?" Peter asked, he was curious. The news didn't really have any answers concerning the situation. The government was trying to keep as much of it buried under the rug as possible.

"Not nearly enough," Agent Coulson sighed, sounding tired.

"How long am I going to have to stay with you guys?" Peter dreaded asking but he was also realistic. He needed to know what their plans were, and whether or not he was going to be forced to make some of his own. He couldn't just stay in hiding from Hydra forever. He had his responsibilities as Spider-Man to think of.

"Hydra knows who you are now, Peter," Agent Coulson began carefully.

"Which means I can't just go back to my normal life. At least not until Hydra's defeated, which I'm not going to hold my breath for. They're like a bad horror movie monster. They're always going to come crawling back from whatever ass whooping they get at the end of the credits," Peter slumped back in his seat.

"That's pretty much a perfect description of them. They're definitely a bench of weasels," Skye grinned at him.

Peter laughed.

"You're going to stay with us for a little while. I'm going to contact your mother, and get some input on what she would like us to do next," Agent Coulson said casually like he hadn't just dropped a huge bomb.

"My mother?" Peter gaped. "Do you mean Mary Parker, mother or like my birth mother, mother."

Peter needed the clarification because he'd set it in his mind that both of them were dead.

"Your birth mother," Agent Coulson regarded him closely, assessing and weighing his reaction.

Suddenly the guy's calm, smooth expression wasn't so comforting.

"She's alive? Shouldn't she be like in her nineties or something by now?" Peter demanded, his mind spinning with possibilities.

"She's 72 actually," Agent Coulson flashed a small, amused smile.

"Seventy-two," Peter mumbled. "So you know who she is. What's her name?"

"Her identity is classified, at least until she gives me permission to tell you. I will tell you she works for SHIELD, and she is the one who asked me to keep an eye on you."

"Why isn't she here?" Peter felt bitterness well inside him.

"She has something she needs to take care of. Neither of us was aware that Hydra was actually planning to snatch you up. We were just there to monitor you, and make sure they weren't in the area until she could come herself."

"If they hadn't been there would you have made contact?"

"No," Agent Coulson stated simply, not pulling any punches.

"Why? Has she known about me all these years and just chosen not to have anything to do with me?" Peter demanded angrily.

"Those are questions you need to ask her. I only know that she cares deeply about you," Agent Coulson said confidently.

Peter silently fumed. He could read between the lines. His birth mother must have known exactly where he was to send someone to watch out for him. Peter had been excited for all of a minute over the fact that he might have an actual chance of meeting his birth mother. Knowing that she'd chosen not to be a part of his life stung.

Where were the brainless thugs that he could beat the crap when he needed them? He could really use some mindless physical task right now to get his mind off the fact that his mother was alive, and had connections with SHIELD.

It did lead him to thoughts about what would happen with him away from the city. He knew it had been doing all right before he'd become Spider-Man. It just seemed like there were more and more powered people coming out of the woodwork lately. Hopefully he could figure something out. Just because Peter Parker couldn't be seen in public didn't mean Spider-Man couldn't be.

The rest of the trip to the super secret SHIELD base was made in relative silence. Peter was still trying to get over just how quickly his entire life had changed, and the fact that his birth was alive out there somewhere. The SHIELD agents each seemed to be lost in their own thoughts. The last month had to have been difficult for them. SHIELD had been completely infiltrated by Hydra. From what he and Gwen had read partners who had worked together for years had turned on one another. It was friends against friends.

Peter leaned back, and tried not to think about what might happen in the future.


Thanks for the enthusiastic response to this story!

This is going to end being more of a mix between the MCU and the Marvel comic verse. I'm pulling ideas from both and trying to mesh them together.

I have the next two chapters already written but I still have a few plot points I need to work before I can post them.