Tony Stark In An Alternate Timeline

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A/N: Sif's decision to stay on Earth weighs heavily on Tony's mind.

-x-X-x-

"I really am my own worst enemy, aren't I Pep?"

Pepper Stark lets out a soft sigh as she runs her fingers through her husband's hair. The two of them are in the living room of Tony's Malibu Residence, with her sat on the couch and him laying across it with his head in her lap. The… events of New Mexico are still settling three days later, and Pepper has to admit that she's still a little rattled even now.

After all, everyone else thought Tony had been wearing armor under his clothes that had protected him from that massive metal monster's attack. Only Pepper and JARVIS knew the truth. Tony had called for J to send the armor over, but he hadn't actually had it on when he'd been struck with the beam.

Instead, when Pepper had gotten to him… there'd been a glowing orange hole through Tony's sternum easily twice the size of the space his old Arc Reactor had occupied. Tony should have been dead, but the Extremis had rapidly regenerated his body, filling in the destroyed flesh and organs. Pepper didn't think she ever wanted to see Tony's heart rebuild itself and begin beating like she had ever again, even if it had been covered up by muscle, bone, and skin shortly after.

Tony had survived. And they'd gotten some of the armor onto him to explain that survival to everyone else. And really, it had all worked out for the best in the end. Thor had gotten his powers back just like Tony had wanted, and for the moment the façade was intact. However, there was just one small hitch in all of that.

"Will it really be that bad, having her around? I know she didn't stay the first time, but is she really that much of a danger?"

Sighing, Tony considers Pepper's question for a moment.

"… It'll get annoying when Thor doesn't come back. I suppose there's a chance that he won't have to destroy the Bifrost this time, but I'm not counting on it. Sif is going to wind up stranded, and the moment that SHIELD and HYDRA realize that she's stuck on Earth with no way home, they're going to start pressuring me for a piece of her."

Pepper frowns.

"They're treating her like a diplomatic envoy at the moment, which is all well and good… but the longer we go without Thor's return, the more they'll start to wonder if he just abandoned her here. And then they'll start to think they can take liberties."

"… You'll stop them, of course."

Tony looks up at that, at her supreme confidence in him. Then, he cracks a grin.

"Of course. I'm not going to let them dissect her, or manipulate her, or abuse her in any way. Unfortunately, me and my big head… I showed her too much."

Pepper winces at that. Tony had told her that he'd been a little more cavalier about his true nature with both Thor and Sif. To say nothing of Loki's dual assassination attempts. She and Tony were perhaps the only ones who knew exactly why Loki had targeted Tony over Thor with that big fucking metal monster. It was because she thought she'd already killed him, and when she found out he was alive, she clearly sought to rectify the issue.

It made Pepper want to punch a hole through a wall, frankly. Or maybe find a way to travel between realms herself so she could grab that goddess bitch by her hair and kick her teeth in personally. Alas, neither of those were really options. Pepper couldn't afford to let her anger get the better of her these days. Not with just how powerful she was now thanks to Tony.

Abruptly, Pepper comes to a decision then and there.

"… She won't say anything."

Tony looks up at her again, raising an eyebrow. Pepper just gives him a smile.

"Call it a woman's intuition. Besides, who would she tell? She has no allies here on Earth… except for perhaps us. I'll have a talk with her. Make sure we're all on the same page."

"Pep…"

But whatever Tony was going to say is cut off by the door slamming open and Maya Hansen's voice echoing through the house.

"Tony? Pepper? Are you both in?"

There's excitement in the scientist's voice, and Tony and Pepper exchange a glance for a brief moment before Tony sighs and gives Pepper a nod.

"Alright, I'll leave it in your hands."

Then, he raises his voice.

"Maya! We're in the living room!"

A moment later and an overexcited superpowered geneticist comes racing into the living room at speeds that a normal human wouldn't have even been able to track. She all but zips over to Tony and Pepper on the couch, dropping to her knees in order to skid the rest of the way across the floor. Grabbing Tony by the shoulder with one hand as she holds up a tablet in the other, Maya's eyes are wide, the woman almost manic. Looking at the both of them, Maya ultimately focuses on Tony.

"Tony… I think I made a breakthrough on Extremis."

What? Pepper's brow furrows as Tony lifts himself off of her lap and sits up. She'd thought Extremis was already completed?

"A breakthrough, Maya? What do you mean?"

Still on her knees in front of the couch, she pushes the tablet into Tony's lap.

"Look! Look at this. I just… I thought I was ready to move on. I thought Extremis was completed and all that was left was tweaking it to dilute it and make still useful but less powerful forms. But something kept niggling at the back of my mind. Something had me going back and doing a bit more tinkering."

Pepper watches as Maya gushes over her work, an affectionate smile worming its way across the red head's face. All that time ago, when Tony had first told her he wanted her to help him seduce the beautiful scientist, Pepper hadn't been sure what would come of it. But now? Maya felt like part of their family truth be told. And Pepper wouldn't have it any other way.

Still, the other woman could get a little excitable at times. And being dosed with Extremis and the Serum had only exacerbated the issue. Reaching out, Pepper captures a lock of Maya's hair in her fingers, and in doing so captures Maya's attention as well when she gives it a gentle tug.

"Calm down, Maya. Breathe, darling."

Flushing a little bit, Maya nevertheless does as she's told. For a moment, Pepper can tell that the other woman is losing herself in Pepper's eyes, growing calmer and calmer simply by virtue of the connection they share. And then…

"This is incredible, Maya."

Tony's disbelieving voice breaks Maya out of the momentary trance, causing Pepper to huff in good-natured annoyance as she leans back and watches Maya reorient one hundred percent of her attention onto Tony.

"I-Is it? I mean, I know I'm smarter now… everything is so much easier to figure out then it was before. But part of me still couldn't believe I might actually be onto something…"

Tony scoffs, eyes still fixated on the tablet.

"More than something, Maya. This is… so far beyond my expectations for Extremis that it's not even funny. With this…"

Pepper raises an eyebrow.

"What is it, Tony?"

Looking over at her, her husband grins.

"Technopathy, basically. Maya has begun developing an upgrade to our Extremis that would essentially give us the ability to interface with and directly control technology with our minds. Forget stuffing microchip implants into our brains, with this we could have it all without any of the true risk. Elon Musk and Neuralink, eat your heart out."

Pepper raises an eyebrow at that. She recognizes the name Elon Musk… a man who she knows wishes he could be Tony Stark with every fiber of his being. But…

"Neuralink, Tony?"

Tony freezes like a deer caught in the headlights and after a moment Pepper does the same as she realizes that Tony had clearly referenced something from the future… right in front of Maya, who did not know about Tony's future visions even now after years of them being lovers.

Pepper had never pushed for Tony to tell more people about everything he'd seen and she didn't intend to start now. If Tony wound up letting more people in on the secret, great. If he never told another soul other than her and JARVIS, also great. Still…

"You know Maya, if you're going to be on your knees down there…"

Going into damage control mode, Pepper turns on seductress like flicking a switch. She gives Maya a raunchy grin, one that has the scientist blinking for a moment before grinning right back. A moment later and Maya is spreading Tony's legs apart, her hands on his knees as she shuffles forward. Tony gives Pepper a look of appreciation and gratitude, and she just gives his shoulder a squeeze as she rises from the couch.

"I'm going to make the three of us some drinks. I'll be right back."

By the time she gets back, Maya is full-blown multitasking, switching between sucking Tony's cock and answering his questions about her latest work with the ease of a woman who had her natural born genius further enhanced by science.

Pepper sets down the drinks and sits back down on the couch, letting the two scientists talk shop as she listens with a smile on her lips. Eventually, things do descend into the truly debauched and depraved, but not for a few hours as Tony and Maya tinker and tool with this new upgrade to Extremis.

Being able to mentally interface with technology… Pepper can already imagine half a dozen ways she could use such a thing in her daily life and she's not even a scientist. Needless to say, she doesn't think it'll take long for Tony and Maya to figure this out. They're both way too excited about it, after all.

Pepper provides what she always provides in such situations… a more grounded presence, to keep the two geniuses from floating off into the clouds together, always ready to bring them both back down to Earth.

-x-X-x-

"Mr. Secretary."

"Director."

As Nick Fury sits down in Alexander Pierce's office, he stares at the man on the other side of the desk for a long, quiet moment before deciding to just get on with it.

"We need to revisit the Avengers Initiative. And we need to start developing weapons that can protect us if the Norse fucking Pantheon comes back any time soon as well."

Behind his desk, Pierce smiles grimly.

"This week was a bit of a shock, wasn't it? Eye opening to say the least."

Nick scoffs, knowing that Pierce wasn't actually trying to make an eye pun at him.

"That's an understatement, Mr. Secretary. We're lucky nobody got hurt. We're especially lucky that all that got damaged was Stark Facility built in half a day. This could have been a disaster, both in terms of destruction and in terms of exposure."

Here, Pierce smiles a bit more broadly.

"Yes, Tony performed quite well didn't he? We were right to place our trust in him. His efforts have left us with an alien visitor to study, an alien prince who claims him as a… heh, 'Shield-Bro', and the destroyed remains of an alien weapon. Your people have secured the automaton, yes?"

Nick nods sharply.

"Yeah, it's been secured. Got some eggheads working on it now. As for Stark… did you know about the armor?"

Here, Fury half-hopes Pierce will be as in the dark as he was and maybe even upset about it. But the way the Secretary's smile widens tells the SHIELD Director that his paranoia has paid off once again.

"I knew, yes. Something that Tony has been working on for the World Security Council and SHIELD for a couple years now. And it's why I'm going to have to decline your request to revisit the Avenger's Initiative, I'm afraid."

Narrowing his one good eye, the Director of SHIELD grits his teeth.

"I'm supposed to be in charge of SHIELD. If Stark was working on something for us, I should have heard about it, right?"

But Alexander Pierce isn't a man who's easily intimidated. He just chuckles as he taps his desk.

"You're hearing about it now, Nick. I'm sorry but until recently it was all very theoretical and thus very hush hush. Couldn't risk this sort of thing getting into enemy hands.

Nick Fury leans back in his chair as Pierce swivels his monitor around to show him what Tony Stark and the WSC had been working on. He stares at the rows of tin soldiers, the shiny armor, and finds himself curious in spite of his immediate dislike of anything Stark related.

"Tony calls them the Iron Legion. Initially they were to be remote piloted, but I convinced him otherwise. One-man suits with the power and strength of a hundred men. More maneuverable than an F-22 Raptor, Nick. Capable of both ground, air, and water missions. Unbeatable by any modern weapons. And just the sort of thing we need our brave men and women in SHIELD wearing to combat aliens the next time they decide to threaten our planet."

Here, the Secretary leans back in his chair and steeples his fingers together with a sigh.

"I know you had your heart set on the Avengers, Nick. But bringing a bunch of antisocial misfits with superpowers together was always a long shot. And between Banner once more in the wind, I'm not sure who you even have in mind for it at this point. But this… we have people in mind for the Iron Legion. Specifically, I want to put the STRIKE Team in the suits. They're our best and brightest after all. Consider how much stronger they'll be flying around in these things."

Fury had to admit… it was an appetizing mental image. There was just one glaring downside.

"Can we trust Stark not to screw us over on this?"

As anticipated, Pierce just sighs and gives Fury an almost wounded look.

"Of course we can, Nick. Tony is a good man. He went through a crucible just like all good men do and he came out the other side wanting to make the world a better place. He's on our side."

"There's still a lot we don't know about his activities, Mr. Secretary. A lot we haven't been able to find out because of his AI. He might not be as good of a man as you think he is."

"Well that's why I pushed for the Iron Legion to be made into suits that would have human pilots Nick! Men we could trust!"

Fury just shakes his head, not placated in the slightest.

"All I'm asking is for a little compartmentalization. Fine. We put the STRIKE Team in these suits. Make them this… Iron Legion. But we don't put all of our eggs in Stark's basket. Give me approval to start researching alternative weapons. Without Stark's knowledge. No consulting. No nothing."

Pierce tilts his head to the side at that before letting out a sigh.

"You want to use the Cube, I presume?"

A memory of one of SHIELD's greatest treasures, a glowing blue box unearthed during their hunt for Captain America, surfaces in Fury's mind even as he nods.

"Yeah. I want to use the Cube. The energy output of that thing… SHIELD might not have been equipped to properly handle it back in the day, but we're in the twenty-first century now. And we're dealing with fucking aliens who can show up on our planet uninvited at any time they want. Time to revisit old treasures, I'm thinking."

Alexander Pierce ponders it for a moment before sighing.

"I'm not opposed to it Nick… but you know Tony could be a huge boon to any research you did with the Cube, right?"

Fury scowls, but the Secretary just holds up a hand.

"… Give me a day to think it over. I'll have my answer for you by tomorrow. For something of this magnitude, I need to consult with my colleagues."

That was probably the best that the SHIELD Director could expect to get, in the end. Nodding sharply, Fury rises from his chair, throwing one last glance at the Iron Legion as he does so.

"… Iron Legion's a dumb name by the way. Is that the best Stark could do?"

Pierce grins.

"You know, Tony said something similar about the Avengers Initiative. Something about naming your superhero group after the concept of revenge instead of protection sounded like a loser's mentality from start to finish."

Fury scowls angrily at that, causing Pierce to raise his hands in surrender.

"He said it, Nick, not me. Don't shoot the messenger."

Huffing, Fury points at the image of the Iron Legion.

"Be careful about putting too much power into the hands of that man, Mr. Secretary. Think about what I said. Get back to me as soon as possible so I can get to work."

And with that, Fury turns and stalks out of the office, thoughts of alien gods and metal suits and mortal men swirling through his paranoid mind.

-x-X-x-

Alexander Pierce watches Nick go for a moment, his expression contemplative. Then, he turns to his monitor and shoots off a ping to Arnim Zola. The veteran Artificial Intelligence responds to him quickly and Pierce outlines the situation to Zola, explaining Fury's proposal and asking for advice.

On the one hand, Tony had definitely gotten results since joining HYDRA. On the other hand, it had never been HYDRA's intention to reveal the Iron Legion to SHIELD. Originally, the suits were supposed to be used by HYDRA operatives for HYDRA missions only. But when Tony had nearly been struck down out in New Mexico and forced to reveal his own personal armor as a result, they'd had to pivot.

It was no big loss, truth be told. The STRIKE Team were all HYDRA anyways after all, so them flying missions as part of the Iron Legion under SHIELD would still ultimately be serving HYDRA's purposes. And it wasn't like it was Tony's fault that he got targeted like that in the end. Given the boon he'd been to HYDRA these past couple of years, Pierce was happier with him alive then dead.

Still… perhaps Fury was right about avoiding putting all of their eggs in Stark's basket. Zola had already assured Pierce that he could easily wrest control of the Iron Legion Network from JARVIS if he needed to, but even still…

There's a ping as Pierce gets a message back from the German Scientist turned AI. He reads Zola's message with a raised brow and after a moment nods to himself.

Even Zola agreed that Stark should be kept in the dark about research into the Cube. In this case, Fury's paranoia was serving him well. If Stark went off the reservation, they would need a way to put him down. It was only good sense in the end.

Shooting off a quick 'thank you' to Zola for his assistance, Pierce then begins drafting a message to Nick granting him approval for the new gambit, to be sent out in the morning. Can't have Nick thinking he made up his mind in just five minutes, after all.

Once that's done, Alexander Pierce sits back in his chair and laces his fingers together over his stomach, a satisfied smile on his lips. Everything was going just as planned. Even this alien attack in New Mexico wasn't enough to disrupt the peace that HYDRA had so far managed to bring to the world. He did so love an orderly planet.

-x-X-x-

A/N: Fury and Pierce trying to plot and scheme behind Tony's back. Except Fury doesn't know Pierce is HYDRA and Pierce doesn't know JARVIS is Zola.

Lol. Lmao, even.

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