Summary
Hydra's Project Insight was a failure, but their Operation Phoenix was not. In a devastating series of events, Tony and Steve are left to build a Resistance out of the ashes and take down Hydra once and for all. However, taking down their archenemy will end up involving much more than a couple of blasts to the head as Tony and Steve's screwed up pasts come back to haunt them. ((Rated T mainly for language and violence))

Warnings
Series: [it's a series of AUs; still needs a title]
Series Number: 1st
Prequel: N/A
Timeframe: Pre-AoU, Post-CA:TWS
Ships: Clintasha, Pepperony
AUish Aspects: Hydra!AU, Deaf!Clint, a bit of Dark/Psycho!Tony, Tony doesn't have his arc reactor removed

Main: Possible spoilers for Agents of S.H.I.E.L.D.! This story will include some strong language and a fair amount of violence. There's also some panic attacks, nightmares, mentions of self-harm, but they're all usually pretty brief. Still, trigger warning nevertheless. Also, be prepared for a lot of whump, angst, and bromance. If any of these things are especially bad in a particular chapter, I'll put a specific warning saying so above said chapter.
Sequel: N/A

Disclaimer
I do not own Marvel, Disney, or the Avengers. If I owned any of those things, I probably wouldn't be sitting here writing this xD.

-Chapter 1: Of Nightmares and Capsicles-

Author: Shadow Wolf Artist
Editor: FanQueen on Fire

"THERE'S NOTHING HERE!" Tony hollered, shooting a repulsor blast at the wall. He slammed his armored fist into the ground. "ALL THAT WORK AND THERE'S NOTHING!"

"Tony, it's okay," Steve said slowly, hiding his own frustration. "Take a deep breath."

"All that work and it was a DEAD END. A DEAD FU-"

"Cap doesn't like that kind of language," Clint chuckled over the com. He, Natasha, and Bruce had all stayed back at the Tower monitoring things while they sent the team's current muscle, namely Steve and Tony (the Hulk was unnecessary, and Thor had yet to return from Asgard), to eliminate Operation Phoenix. According to their intel, the secret Hydra project had hardly developed and was in a low guard facility (so not to draw attention) disguised as a government science lab, so taking it out would be a cinch. Well, that same intel had led to an empty, rundown building in the middle of nowhere, and now everyone was a little frustrated; Tony was just the only one who let it show.

"I'm so done with all this bullshit," the billionaire seethed. "I'd like a legitimate lead just ONE TIME!"

"Look, Stark, I get this is frustrating, but you need to cool your jets. Come back with Steve and we'll order a pizza or something," Natasha commanded calmly.

"We have no idea what threat Operation Phoenix possesses, and we apparently don't have any valuable intel on the damn thing. This is hardly the time for pizza and de-stressing. Also, the last time I had pizza to 'de-stress,' my lifeline was ripped out of my chest and I almost died."

"C'mon, Tony. It'll make you feel better," Bruce chimed in.

"And we promise not to touch your arc reactor and try to kill you while you're pacified by pizza. Besides, I think Pepper is lonely," Clint added. Somewhere in the background, Tony heard the redhead yell a disgruntled reply, but it was so muffled that the genius barely heard it. He smiled inwardly nevertheless. Steve turned to Tony, shrugging and gently cocking his head.

"They're right. Not every mission can be a success," the super soldier sighed, shifting from foot to foot.

"Not every mission has the fate of the world in the balance," Tony replied bitterly, his brief moment of sweetness lost.

"Oh come on. For all we know, Operation Phoenix is just some stupid Hydra experiment that's doomed to failure," Steve argued.

"Just like Project Insight was some stupid S.H.I.E.L.D. project that was meant to help the world. Look, Steve, this could be serious."

"Or it could be nothing. Since when are you the serious one?"

"Would you two just get a room already?" Clint groaned over the com. "Bicker on the way home. Nat's not ordering food until you two get your asses back to base."

"Fine. But I'm not sleeping until we find out what this whole Operation Phoenix is about, and stop it. Also, if you're ordering pizza, I want Hawaiian," Tony replied, starting up his thrusters.

That's when the screams started.

They filled the coms, and Tony nearly ripped his out as the high pitched noises assaulted his eardrums. "What's going on? What's happening?!" Steve cried, running to the small jet he had used to get to where Operation Phoenix had supposedly been. Tony was already in the air.

"The Tower- holy shit all of New York- wait what the- YOU LEAVE HER ALONE- NAT HELP-" Clint's choppy voice sounded in Steve and Tony's earpieces, filled with fear and desperation. Then, silence. Muddled chaos could be heard in the background, but Clint's voice had gone dead.

"CLINT? BRUCE? NATASHA?! ARE YOU THERE?!" Tony yelled into his com. No response. "WHAT'S HAPPENING?! SOMEBODY ANSWER!"

By the time the duo had gotten back to New York, they realized they were too late. Miles out, they could see that something was wrong, and as they got closer they saw that fire had engulfed the entire city, twisting spires of red and orange and yellow consuming everything in its path. It would've been beautiful had it not been so terrifying, so hellish. Like a scene straight from a nightmare, Tony watched as his entire universe was ripped apart, a sickening knot growing in his stomach as he shot to the Tower. The once magnificent home base for the Avengers and their companions (namely Pepper, and sometimes Rhodey) was nothing more than a burning torch, fire bursting through the windows and out the roof, devouring anything and everything it could. Somewhere in the back of his mind, though he realized it could've been J.A.R.V.I.S. or even Steve screeching in his ear, Tony knew what he was about to do was suicidal, but he couldn't stand by and watch his home simply be brought to the ground. He shot through an open window, trying desperately to quench the flames, screaming the names of his friends and teammates: Pepper, Bruce, Clint, Natasha- they were all still inside. J.A.R.V.I.S. was hollering at him, alarms blaring, telling him to get the hell out of there. He was overheating at an alarming rate, and preliminary scans showed that this fire was nothing like anything the A.I. had ever seen before. It was a mutation, an actual hell, something that shouldn't exist. Pieces of Tony's suit were splitting apart and bursting off his body, results from the strange flames accompanied with all of the suit's systems shutting down in ways the genius didn't even think possible. Soon it was just him, in his cotton t-shirt and jeans and sneakers, running through the flames, trying desperately to find his comrades. Tony screamed until his voice cracked and broke, tears stinging his raw face as the salty water flooded his eyes and spilled over. No one. No one was there. Agony suddenly took hold of his hands and forearms as fire licked the genius's tender skin, burning and scarring his flesh. His vision was blurry, his body in crippling pain, and with one final cry for Pepper the billionaire fell to his knees, unable to get up. Heat seared his skin, and he tried to cry out but no sound left his dry throat. He was alone. He was going to die, and he was going to die alone.

Somewhere, through his last shreds of consciousness, Tony heard his name being yelled over and over, getting progressively closer to his limp form. He forced his head off the ground, and saw Steve standing over him, blue eyes blazing with fear. The super soldier grabbed him, and the genius went limp as Steve leaped from the burning building into the small jet, slamming it into gear and flying away from the devastation as fast as he could. The captain looked down at the destruction, praying for survivors that he might yet be able to save, and nearly vomited at what he saw. The delirious billionaire followed suit, and bile rose up in his throat, accompanied with a scream of pure defeat and anguish.

The fire had twisted and weaved and engulfed everything but certain spots in the pavement, creating an image that would be forever burned into the two men's minds. The destruction spelled out two words, words that would forever scar and torment the two lone survivors of the holocaust that had been wrought.

"Operation Phoenix."

Tony woke up in a cold sweat, shivers wracking his body, the nightmare still painfully fresh in his mind. He glanced over at Steve's portion of the room and saw that the super soldier was sleeping peacefully in his bed, his chest softly rising and falling. The genius fumbled out of bed, trying to get to his own room before he completely lost it as he so often did after such a vivid, hellish nightmare. Phantom agony engulfed his hands before he got there, and he gave a sharp gasp before he could stop himself. Instantly, the captain was on his feet (damn your super soldier hearing), running over to where the philanthropist had crumpled to the ground. He knelt down and wrapped his arms around Tony in the way that one does when their friend is experiencing a panic attack, trying desperately to calm the genius like a parent calming a frightened child. "Hey, it's over. There's no more fire, Tony. You aren't burning. You're in our room in the base, okay? Focus on that. Don't focus on the fire."

"Operation Phoenix," was all the genius could manage in reply. There were so many things he wanted to say (such as "Steve get your hands off me the Rebels think we're gay already" or "Dammit Rogers as much as I like being fondled you're just making it weird"), but panic had overridden all the logical parts of his brain, and he couldn't do anything but spit out those two forsaken words.

"Yeah, I know. Hydra is a pain in the ass. But you aren't there now, you aren't back in New York City, you're here in our base, in our room."

"You know, if a Rebel came in and saw this, the gay jokes would never end," Tony sputtered, finally regaining control of his mouth. His hands still refused to cooperate, and they were shaking madly, but at least they weren't burning with a phantom agony anymore. Laughing at the genius's crude joke, Steve took Tony's hands in his, rubbing his thumbs over the backs of the genius's shaking fists, trying to get them to stop trembling. The rough, scarred skin that passed under his thumbs was a sick, twisted reminder of the day that had ruined their lives, the day where they had found out what Operation Phoenix meant, the day where they had lost the world to Hydra.

The super soldier was pushed away as Tony got to his feet, brushing himself off with his still shaking fingers. "I'm fine, Rogers. Really." Steve opened his mouth to argue, but then their alarm went off, signifying that it was 05:30 and it was time to start the day. Groaning, the philanthropist stretched, stumbling out of Steve's room and across the hall into his own room. His charred fingers drummed on his arc reactor as he searched for his white cotton tank and loose shorts. In the middle of pulling on his pants, the genius heard a knock on his door, and he rolled his eyes; the knocking was the resident super soldier boasting the fact that he had finished changing first. Tying his sneakers, Tony pushed open his bedroom door and was greeted by a humorous snort from Steve.

"Ha! Beat you," he sneered.

"Shut up, asshole," the genius grumbled. Suddenly, before Steve could register what was happening, Tony took off sprinting down the hallway, nearly falling over as he took a sharp turn. The super soldier caught up easily and passed the philanthropist in their unspoken race toward the gym. By the time Tony got there, Steve had already started his push-ups.

"Rude. You're supposed to wait for me," the genius pouted, dropping down next to Steve and falling into rhythm with the captain's push-ups. The super soldier slowed his pace just a little bit so that Tony could keep up.

"You were taking too long," Steve chuckled. Tony stuck his tongue out at the captain in response, ignoring the fact that his hands and lower arms were starting to hurt, with actual pain this time. Push-ups had never really been good for his damaged hands, but he did them anyway to keep his strength up. Steve had repeatedly suggested physical therapy, and Tony had repeatedly replied by saying he was too busy, and "besides it's not like we have a physical therapist on staff."

"You should really go see one of the doctors, Stark," Steve said rather abruptly, completing push-up 136 and breaking the silence that had swallowed up the other 135. "I'm sure Simmons could help."

"No. My hands are just a painful reminder of the fires, and I can't imagine flaunting them is gonna do anyone any good," Tony replied, dropping into push-up 138.

"Everyone sees them when we go for our run," Steve argued, completing push-up 141, "and no one has freaked out yet."

"We're moving too fast," Tony chuckled. "No one is really up at this hour anyway." He took a deep breath. "Look, Rogers, I've got a solution all figured out; stop fretting. You know there's a reason I wear the gauntlets all the time."

"And everyone thinks it's because you're paranoid."

"Well, they aren't entirely wrong." Tony let out a huff as he completed push-up 150. His hands threatened to spasm, so he paused in his push-ups to let them do their thing before continuing the morning routine. "Steve, my hands shouldn't be what everyone is worrying about. We need to focus on more pressing matters, namely Hydra, Operation Phoenix, what the hell they used to burn the world down, so that we can develop something to stop it should they use it again. We've had 3 ½ years to work on this, Cap, and we have no idea what it is, where it came from, or when they plan on using it again. We don't even know where Hydra's base is, and you think we should be worried about my hands?" The genius paused to take a breath. "Do you know if Fitzsimmons has made any progress? On the fire, I mean."

Steve sighed, staying quiet a millisecond too long before answering (Why do I feel like he's hiding something from me? Partnership isn't about keeping secrets, Spangles). "They have a lot of hypotheticals, but nothing's definite yet. They have incredibly limited samples and data to go off of, limited equipment to use, and they have the great majority of their Division-"

"Working on biological weapons for the Resistance yes I know. I'm kind of the one that told them to do that," the philanthropist interrupted, his tone almost bitter. Silence ensued, and it wasn't broken until they completed their 200 push-ups. Sitting back to take a brief rest, the duo took turns drinking from a single water bottle (after lots of teasing from the resident genius, seeing as in his rush to beat Tony changing, Steve had completely forgotten about his water bottle), and when they were done the super soldier dared to break the silence again.

"What have you got on your schedule today, Commander Stark?" he asked, starting their daily 200 curl-ups.

"I'm meeting with the Science Division in 2 hours, and by that I mean Fitzsimmons, teaching a robotics class at 16:00, and I believe Coulson wanted to speak with both of us after dinner. You?"

"May asked me to teach the gym classes today. She wanted some time to herself," Steve replied, pulling into curl-up 7. 183 to go.

After completing their curl-ups, and then their pull-ups, and then all the other various stretches and exercises they started their mornings with, the two Resistance leaders went for their morning run around the base. It was inside, of course, but seeing as only a select few got up at this hour the duo didn't have to worry about running into anyone but each other as they dashed down the halls. They ran in silence, sweat staining their shirts as they jogged down the hallways and corridors that made up the Resistance base. Steve's mind was on how he used to do runs like these with Sam, and Tony's mind was on Pepper and the team he had let burn. He often (read as: always) blamed himself for their deaths, seeing as if he hadn't been bickering with Steve he might have gotten back in time to save them, or even stop the fire entirely. Then they could've ordered pizza, 'de-stressed,' and saved the world like they always did. Why hadn't they been able to this time? Hydra had never bested them before, and the fact that they had only succeeded because Tony couldn't shut his damn mouth made the genius sick. And, he couldn't lock himself away in his lab like he always did when things went wrong because there was no lab. There was no Tower. Even if there was, he wouldn't be able to do the fine detailed work he had always done when he was stressed; his hands were ruined. He couldn't mourn, because he was busy running a Resistance to make Hydra pay for all they had done.

Tony didn't realize he was panicking again until Steve grabbed his hands and forcefully stopped their run. "Stark. Calm down."

"Sorry, Capsicle. It just isn't my day today, is it?" the genius sighed. Steve sighed in response, letting go of Tony's hands and waiting for the philanthropist to start running again. Tony so rarely used the 'Capsicle' nickname anymore, and whenever he used it it was to try and lighten the mood (it usually didn't work). The genius's hands had stopped trembling, and he started to run again, trying to shove all the thoughts about the fire from his mind. Steve resumed jogging as well, staying in stride with Tony instead of running ahead like he usually did.

After their run, the duo returned to their separate rooms to shower and get dressed. Tony checked the time, confirming that he still had a half hour before he was to meet with Fitzsimmons and the Science Division, and then proceeded to strip himself of his sweaty workout clothes and step into the shower. The cold water felt good against his warm skin, though he refused to let it touch his face, seeing as whenever it did he had a tendency to respond negatively (and, after being waterboarded with freezing, filthy water, who wouldn't?). He sharpened the edges of his goatee ("Just because the world is run by Hydra now and we're busy running a secret rebel organization doesn't mean I should abandon this sexy look, Steve"), combed his hair, and put on his more casual attire, which consisted of his gauntlets, camo cargo pants, a white t-shirt, a bulletproof black vest, and his uniform hat because he felt like it. On second thought, he decided to throw on his actual uniform so that he might actually look presentable when he met with the Science Division. He changed into navy blue pants and threw the matching jacket over his shirt and vest, then slipped into a pair of black boots and straightened his hat. Stepping out, he found with pleasure that he had beaten Steve in showering and changing, and the genius decided to wait outside of the captain's room until the super soldier was finished so that he could flaunt his victory face-to-face.

"Fitzsimmons! You wanted to see me?" Tony announced his presence boldly, stepping into the room exactly at 08:15, and everyone quickly turned and saluted. The genius waved his hand, telling them to put their hands down (his reason being that he was not worth saluting, and that they should save it for Steve or something), and made his way over to where the scientist duo was arguing over who should speak first. He watched with an amused detachment, reminded of how he and Bruce used to bicker over just about everything when they were working in the lab. After a few moments of hushed 'quarreling,' as Simmons liked to call it, the inseparable pair turned to face their commander. "Sorry for the sudden meeting, sir, but I think you would be interested in Fitz's theory as to what happened regarding the fires. Working off of such limited samples, this is just a hypothetical at this point, but it's the best we've got." She paused, passing the speaking off to Fitz.

"My theory, sir, is that large amounts of people, most likely Hydra devotees, acted as Japanese kamikazes from WWII, 'sacrificing themselves for the great good' and all that. What I'm alluding to is that these people formed a network or a system of some kind to optimize damage, and then when they were in position-"

"They lit themselves up." Tony finished, his voice scarcely above a whisper.

"Indeed, sir. This would explain how mass fires were able to go off all around the world in incredibly specific locations simultaneously," Simmons further explained, her expression grave. Fitz merely nodded.

"Do you...do you have any hard evidence that might prove this theory?" Tony asked, clearing his throat. The thought that people would willingly give up their lives for Hydra made him sick, and he really just wanted to go lay down for a while. Today just wasn't a great day for the worn down genius.

"Until we know what that fire was made of, we really can't prove any theories," Fitz replied. "And it's nothing like we've ever seen before." Except it is. Kinda Sorta. Maybe. Bloody hell, you have orders, Leopold; stop doubting them and keep your mouth shut. And stop using Simmons's British mannerisms.

"We do have some good news!" Simmons said rather abruptly, quickly changing the depressing topic to a much more cheery subject. "I believe we've developed a system that is much more efficient for growing crops down here. If we may, sir, we'd like to show you!" the British scientist said rather excitedly. She and Fitz led the philanthropist through the Science Division laboratory, chattering on about the project along the way.

"Through studies of how different kinds of artificial light interact with plants-" Fitz started, but was quickly interrupted by a very excited Simmons.

"And water. We also studied how they interact differently with various types of water, including mineral water, purified water, rain water-"

"We also experimented with different types of soil!" Fitz threw in.

"We believe we, and by we I mean the Science Division, have found the perfect combination for growing underground crops that are healthier and tastier. They also grow quicker than the way we are currently growing crops-" Simmons continued.

"But we would like your approval before implementing our methods properly. Tell us if there's anything to fix, change, etcetera." Fitz then pushed open a door at the back of the lab, revealing a room full of plants at all stages in development. Simmons led Tony over to the healthiest, most well-developed looking plant. "This is the kind of growing we wish to implement, and this-" she paused to point at a plant that was about 2/3 as developed as the other one, and less-healthy looking, "is what we're growing now."

"We believe this system would also help grow the grass for the animals, and keep them healthier," Fitz added, coming up behind Tony and Simmons.

"Consider it done," Tony said, waving his hand in approval.

"Thank you, sir!" Simmons said gleefully. The commander gave a lopsided smile, before nodding and turning to walk out. The Science Division saluted him again as he walked out, including Fitzsimmons, and Tony merely shook his head, trying to wave their hands down.

"Please save the niceties for someone who appreciates them," he said, the door closing behind him.

He had hardly walked a few feet before a guard came up behind him, asking to speak with him. "Commander Stark, we have more people seeking refuge. They're in quarantine now, undergoing the standard process."

"Who?" Tony asked sharply. Every time he was approached with this kind of information, he prayed it was Rhodey. He hadn't yet been able to make contact with his long time best friend, and it concerned and worried him to no end. The lieutenant had been on a mission far from where any of the fires had taken place, and Tony clung to that, despite it having been 3 ½ years since he had last spoken to his Rhodey.

"Family of four: mother, father, and two twin 8-year-old daughters. No pets."

"How much of the process have they gone through?"

"It's been confirmed they aren't undercover Hydra operatives, and they're being medically treated now."

"Place of origin?"

"They were living in a town not far from here when Hydra decided to attack them. The Patrol found them 'camping' out in the woods."

"Any idea why Hydra decided to attack them?"

"No, sir. The family is still a little shaken. We believe the attack may have been to remind the world who's in charge."

"Yes, because it certainly needs a reminder," Tony growled sarcastically under his breath. "Sounds like something the bastards would do. Illnesses?"

"None."

"They're okay with me if those putting them through the procedure are okay with them. I'll have men start preparing a room. You are dismissed."

"Yes, sir," the combatant nodded, saluting and marching off. Tony waited until the guard had disappeared down the hall before slamming his armored fist into the wall.

"Dammit Rhodey. Where are you?" he asked softly to no one.

After having men go prepare a room for the incoming family, Tony went back to the Commanders' Quarters, as everyone called them, and flopped on the bed in his own room. He checked the clock, and saw that it was only roughly 9:00. He still had 3 hours until lunch, and then another 4 hours after that until he had to teach a class. Many people at the base thought that lazy days like these were like godsends to the commanders, who were usually crazy busy, but it was days like these that the philanthropist hated most. When he had things to do, he could keep his mind off of the more depressing and frightening thoughts that often plagued him while he slept. Not having anything to do was simply inviting them to invade his mind.

Tony pushed himself off of his bed and changed out of his uniform and back into his baggy, camo cargo pants, kicking off his shoes and shedding his jacket as he did so, leaving only the white t-shirt and the bulletproof vest. He collapsed back onto his bed, sighing loudly as he did so to fill the suffocating silence. He hadn't slept in this bed in forever, seeing as he always slept in the one he had put in Steve's room. The philanthropist pulled off his gauntlets, examining his burned hands as he held them above his head. "Not your fault, that's what Steve always says. Well, what does he know?"

Tony didn't realize he was waiting for a response to his softly spoken words until there wasn't one.

It had been 3 ½ years and he still couldn't get over the fact that J.A.R.V.I.S. wasn't there.

The A.I. wasn't commenting on Tony's ruffled shirt, wasn't trying to comfort him with his robotic concern, wasn't listing off the genius's various injuries and ways to treat them because he wasn't there. He had always managed to soothe Tony, had always managed to talk the philanthropist down off the cliff when he was losing it, but he wasn't there now. He had died in the fire with Pepper and Clint and Natasha and Bruce. Tony was alone, and it was killing him.

-To Be Continued-

A/N: Whoop, here's the first chapter! How was it? A lot of introduction and exposition, I know. It was actually going to be a lot longer (as in I was going to stretch it to them meeting with Coulson after dinner), but I decided that no one would have the time or patience to read that in one sitting (myself included). Also, because I know someone is going to ask this, I DO NOT SHIP STONY. I'm a hardcore Pepperony shipper :D The two (jumping back to Steve and Tony) are incredibly close, yes, seeing as they've had pretty much nothing but each other for 3 ½ years, but I don't ship them. At all. I have nothing against people that do, but...just...no. Uhhhhh I'm probably forgetting something...
Shout out to my friend FanQueen on Fire for editing this! (Also, according to her, Tony is a nugget)
Stop being so suspicious, Steve. You too, Fitz.

~Shadow Wolf Artist