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Five times Steve sensed something unsound about SHIELD (and one time he identified the source)

Summary:

The thing about having enhanced senses, especially when no one else seems to realize that, is that you sense a lot of things no one would expect you to. You find out information that agencies like SHIELD would do anything to hide. And sometimes, you uncover horrible things hidden within the agency one of your best friends during the war founded.

But luckily for Steve, he's got the Avengers by his side, willing to accept what his enhanced senses have noticed, and to help him whatever is going on with SHIELD.

Notes:

I'm not dead, despite promising to post this almost a year ago. For those who don't know, this is a companion fic to my fic "Ten times Steve seemed inhuman (and two times he was all too human)", where the chapters take place in both fics. There's a timeline in the series description in case you're confused. When I started posting it, planning to post weekly, I had finished typing it up, and thought the chapters only needed editing, but because my writing skills had increased since I initially wrote it, I ended up completely rewriting the first chapters before I posted. Of course that led to my next chapters needing even more polishing, fixing of plotholes, and detail adding, so much so that I stalled out on posting. But now, I have rewritten all but the last four chapters, and completely finished editing three, so I should be able to finish posting this on a weekly schedule. Hopefully.

If this is the first chapter of this series you're reading, you should read the first two chapters of the other story, "Ten times Steve seemed inhuman (and two times he was all too human)" before starting this one!

That aside, a WARNING, this chapter, and some of the following chapters will have mentions of rape. There will be absolutely no graphic depictions, and no flashbacks to, or POV of an actual scene of rape. The Avengers only know that rape has happened to a prisoner (that they don't know is Bucky) by SHIELD agents and are determined to remove him from the situation as soon as they know. The other story in this timeline is a lot fluffier, and if you're reading that one and don't want to read this one, which is generally darker in tone, just let me know and I'll provide a summary of what happened in this chapter. There are absolutely fluffy and fun moments in this story, but it's just on average darker than the other one. Also, if there's any tags you feel I'm missing, please let me know!

Comforting scents:Present takes place before this fic in my new timeline, though they can be easily read out of order.

(See the end of the work for more notes.)

Chapter 1: Scent

Chapter Text

Tony was getting along better with Steve recently, which was the only reason he had been working on Steve's suit design. He had a lot of work to do on his own suit, make it stronger, faster, more effective, better. And yet here he was, agonizing over the design of Steve’s suit. Not as a quick distraction from his own suit, playing with concepts and materials. No, he had gone into in depth research in high tech fabrics and combat suits. He used some unique materials in his own suit of course, but nothing like this. 

 

And yet, Cap was using the untested, only mostly finished, prototype on his practice mission for SHIELD! Sure, the outfit he wore for the battle of New York was an insult to good taste, practicality and safety in every way, but to go so far as to steal an unfinished prototype uniform from him to go on a impulsive test mission for SHIELD, when just days ago he had mentioned to Tony that he wasn’t sure he trusted them?! 

 

Tony was furious. He had almost thrown his coffee cup at the wall in frustration once JARVIS had told him what Steve had done when he saw it missing just that morning.

 

He had told Steve he could test the prototype out, see if he had any helpful info, based on how it worked for him, but he had specifically told him to just use it in the gym, that it wasn’t done yet! 

 

He distinctly remembered not quite finishing up a seam before leaving to head to the evening's gathering in the common room. JARVIS had told him Steve had sewn it up before he headed out, but still, there might have been other not quite finished spots he hadn’t noticed! He would not let Cap's perspective of his suit making capabilities rest on an unfinished prototype suit being taken out into presumably full battle! 

 

All he could manage to do after he noticed the suit was missing (several hours after it had been taken in the early morning) was to turn the blueprint for the suit around and around, poking idly at it, wondering where its weak points were. Actual experience in battle found way more weak points than regular testing. What hidden weak points had he not noticed yet? 

 

But SHIELD probably already had a better suit for Captain America, Tony thought bitterly. He had no clue why they allowed that first calamity of a suit, but surely they learned from that mistake after seeing how destroyed his suit had been by the end of the battle. Or maybe they hadn't learned anything, and let Steve use an unfinished prototype made by someone who made metal armor, not super suits. 

 

This was why Tony needed to focus on his own armor. He'd seen some things almost exactly like that in his dreams, the aliens tearing up Steve’s uniform, which had flashed between his terrible uniform from the battle, and the fuzzy sweaters he was wearing all the time now. The armor needed to be better, to stop that from happening. He couldn’t fail him with his miserable excuse for a suit. 

 

It had been Natasha of course, that conniving, sneaky… jerk. Steve had come out of a conversation with her just a day ago and headed straight for the gym he had just begun renovating to be more challenging for the more enhanced members of the team and the super spies, and hadn't come out for way too long. And then he had told Natasha he wanted to go on missions as soon as possible, when before, he had been hesitant. And now they were going on a mission almost immediately, with minimal preparation. He had been oddly… disconnected during last night's gathering too, stiff and tense. Tony had taken pride in luring him into feeling relaxed in the tower, instead of being stiff and formal like he used to. He even seemed to like Tony now, and now Natasha and Clint would probably be telling him all about the ways he was untrustworthy and not recommended.

 

“Sir, Captain Rogers is requesting permission to enter the workshop,” JARVIS interrupted. 

 

“Uh, sure J,” he replied, hoping that Steve wasn't here to throw the new suit in his face, but he didn’t have very high hopes.

 

The music volume lowered, and Steve walked in as Tony spun in his chair to face the door.

 

He… did not look good. He was in an almost aggressively formal button up and slacks, yet his hair looked wet and messy with sweat and grime, his clothes were disheveled and he looked shaken.

 

“What's popping Cap?” He asked, trying to defuse the tension he could practically taste in the air. “Is the prototype suit you stole not up to your old timey standards?”

 

“On the helicarrier, you said you accessed SHIELD's files. Did they notice and shore up their defenses?” 

 

Tony blinked in surprise. That almost sounded like an accusation, but that question… something about it sounded very serious, almost grave. Whatever was happening was nowhere near what he expected. 

 

“Depends on why you want to know,” he said casually. “If you’re asking to accuse me of anything, I only skimmed the tops of their files from their own computers, which only made it that much easier to get in-” 

 

“Can you do it again, but from here?” Steve asked, almost more stern and stiff than before. 

 

“I retained all the information I could,” JARVIS said coolly. “I can certainly access all saved data, and possibly provide more with the codes and passwords I also picked up. Though I will not provide them unless you have a reasonable reason to access that information.” 

 

“You were all mad about me accessing their stuff on the Helicarrier though,” Tony said, spinning again in his chair to hide his unease. 

 

Steve finally seemed to show an emotion that wasn't stiff formality, a flash of shame on his face. “I was mostly mad about the Tesseract guns and took it out on you with Loki's staff amplifying my emotions. I'm sorry.” 

 

But he wasn’t swayed from his goal and continued, “the information I'm looking for is on a certain STRIKE team and their missions,” he said, still stiff and formal.

 

“If you merely intend to snoop, I must turn you down,” JARVIS said formally. “However, I must assume that isn't your intention.” 

 

“Why else would he need that information though?” Tony asked JARVIS. 

 

Steve took a breath, a muscle in his jaw twitching with how hard it was clenched, and said stiffly, “I suspect that STRIKE team Alpha is either not as regulated as they should be for such a highly skilled team with their high clearance, or some higher up is fudging info so that team can do things that go against SHIELD’S goals on SHIELD’S time.” 

 

Something about the dry formality in his tone, and his disheveled appearance sparked the knowledge that this wasn't something said on a whim, or just a feeling something was wrong. He had likely been reciting it in his head for a while, and was deadly serious. That kind of formal and overly precise language was the same kind as Pepper would use when having a very important meeting about something very bad. Like when she broke it to the board that Obie had tried to kill Tony. Not only that, but Steve was angry. Tony realized that he was holding himself so stiffly to restrain himself. To stop himself from going after whoever STRIKE team Alpha was right now. This wasn't just ‘taking an extra break on company time’ kind of unpleasantness, this was ‘lawsuit and probably criminal charges’ serious.

 

“What do you need to confirm those suspicions?” he asked seriously, turning to his screens so he could start doing whatever Steve needed to confirm his information.

 

“I'm not fully sure,” he said quietly, pursing his lips. “it's not… I don't know how to find that information. I know military type organization and files, but SHIELD's higher secrecy and computers… I don't know how to work with that.”

 

“Then that's where I come in,” Tony said proudly. “Pepper is much better than I at the finding discrepancies in the paperwork part, that's part of why I promoted her to CEO in the first place, but I'm really good with the hacking part and JARVIS isn't bad at scanning files for discrepancies.”

 

“What sort of discrepancies are you looking for, and what information triggered this investigation?” JARVIS asked. “I would guess it wasn't financial information.”

 

Steve stiffened again, and Tony wondered what he could have possibly noticed at SHIELD that could ratchet him up this tight. Had he thought he could get by without mentioning why he was suspicious? Tony would do it with Steve that serious, but JARVIS wouldn’t let that happen without a good reason. 

 

“You know I have enhanced senses,” he said bluntly. “Especially smell. I notice nuances any other person would never even think to smell for. That people would never think they would have to hide. My trial mission took place while STRIKE team Alpha was on a separate mission. I bumped into them in the changing room before I showered.” 

 

So he hadn’t even showered after the mission, and had just rushed out of SHIELD as soon as possible. Probably just tossing on whatever clothes he had in his locker. A feeling of dread was rising as Steve snapped out those short, concise sentences. Tony turned around to look at him, to try to make sure he understood that his full attention was on him.

 

“They were heading in from the mission, still bleeding and in their uniforms. They had only wiped down on the way back. And yet,” Steve said, voice going down into almost a growl. “They reeked like someone else's pain and fear, and sex.” He bared his teeth in a vicious snarl, paired with a vicious glare, staring right into Tony's eyes. “They reeked of rape.

 

Tony nearly jumped out of his seat as Steve sharply turned in place and began to pace, teeth still bared in a vicious snarl, shaking with anger. He didn't want to ask if Steve was sure. He'd rather not have that barely restrained anger loosed on him. 

 

“I hate to doubt your observations,” JARVIS said politely, being timely as usual. “But that is a very big accusation to make off just a scent, and may push my privacy protocols if there is reasonable doubt to your accusations. Is it possible that they were merely in the presence of frightened civilians, then on the way back had some… personal time?” 

 

“No,” Steve said roughly, but he took a breath and stopped pacing to face Tony. His face was grim, but a little less rageful. “For one, I did some investigation of my own, and their mission was infiltrating an enemy base where there should've been no civilians, and no prisoners were recorded. For another…” he paused and took another heavy breath, closing his eyes and letting his posture loosen slightly. “That kind of fear and pain, the strength I smelt it at… you don't get it clinging so deeply by just being in the vicinity of the victim briefly. For it to cling so deep, it needs to be transferred by fluids like sweat or blood or… other things, rubbed into fabric and skin with lots of close contact. Scent that deep-” his voice broke slightly, and he turned his head so he wasn't looking directly at Tony anymore. “Scent like that clings to torture chambers and the torturers, not the rescuers.” 

 

Tony found himself struck silent by his emphaticness. Had he smelled something like that after the cave? Would Steve have smelled his own fear and pain and helpless rage after Yinsen died and he had escaped? The wild, terrified joy of his first flight once he had been rescued? 

 

No wonder he was so fierce about this. If he could smell stuff like that, and understand what it meant… “How did you learn that kind of thing?” He blurted out, mouth dry. 

 

“My team raided a lot of Hydra bases,” Steve said dully. “Sometimes there were prisoners, human experimentation. You learn fear scent and all its variants well in war, especially against Hydra.” 

 

“And the… other thing?” He questioned, not quite able to bring himself to say the word. Not with memories of the cave so close, and the possibility of what his captors could have done to him when he was so weak stuck in his mind. 

 

Steve smiled, brittle and a little sharp, baring his teeth. “Some of the villages we traveled through were scared of the soldiers on both sides, and for good reason. None of the Howlies were like that, thank God, but I've threatened more soldiers from our side with my shield than I should've had to. I saw too much of that in London for my taste.” 

 

Tony hadn’t thought… of any of that when he thought of Captain America and the war in the past. He just remembered what his father said, and all the posters and stuff he had from that time. Brightly colored or black and white, and all too vague. He knew logically the horrors of war, especially after all the middle of the night research he had done after his capture, but he hadn’t thought of applying it to Captain America, or his father’s glowing ideal of the war. And what else had Steve seen in that time that his father had simply ignored in his exciting stories?

 

But Tony refocused. That wasn't the most important thing now. What mattered most was confirming those indiscretions, and making sure the STRIKE team Alpha didn't get away with it. They had information to find. And to do that, Tony needed more background.

 

“So by the way you said it, you think this wasn't just a one time thing where they managed to sneak away from surveillance, this is a consistent behavior, and thus something someone up high would probably be covering up.” 

 

“Yes,” Steve said firmly. “The scent of the victim was-” his lips tightened, and he grimaced. “It reminded me of some experimental subjects of Hydra, almost… resigned. In pain, scared, but used to it. Like they can't figure out how to get away, and have… stopped trying.” His voice cracked a little on the last word, and he shook his head. 

 

“That’s a bleak picture,” Tony said grimly, moving to the sparse files on the STRIKE teams that JARVIS pulled up, and quickly clicking through them. “But yeah, if they were making any detours on SHIELD’s fancy proprietary transport, someone would know,” he rambled, trying to distract himself from the flashes of Yinsen's resigned face in his head. “And it would be very hard to drift away from the mission while actively on a highly monitored SHIELD mission, with comms on all the time, and so many people keeping track of making sure the mission goes alright, not just the higher up who might be covering for them. Was that scent clinging to all of them, or was it just one or two?” 

 

“At least most of them, but probably all of them,” Steve said grimly. “I can't be completely sure though, because once I caught a whiff, I was more focused on not taking a swing at them.” 

 

“Makes sense,” Tony replied absently. “If it was more than one or two, it's nearly impossible that they could sneak off unnoticed by the others during a mission. It has to be a separate stop between the mission and SHIELD, where they might be keeping someone… if I can wrangle some likely locations from these files-” 

 

“Thank you Tony,” Steve said fervently. Tony turned around, to catch his eye. He looked a little less miserable and more eager for action. Hopefully he could find something for Steve to help with, because he knew that eagerness to act all too well himself. He didn’t think Steve would start blowing up weapons if he had to wait too long, but he supposed you never knew. 

 

“I'm glad you don’t think it's an insane conclusion to draw. I won't sit back and let that happen if at all possible, but I have a lot less options by myself. I just… the more I learn, the more sure I am that something is wrong deep in SHIELD. Making Tesseract weapons, and now this… it’s worrying. Especially with so many potential ramifications if they’re caught. It has to be something more than just sex if there's so much planning going into it, with potentially an entire secondary location to do the deed…”

 

“Agreed,” Tony said, turning away from the screen for a second. “Who knows how high up the person covering this up is. And why they are going to so much effort to hide it. It could be a one time thing somehow, but it also could be-” his voice broke slightly as he thought of Obie, smiling genially at him as he sold all his weapons to enemies under the table. “really deep in SHIELD, and really high up,” he said weakly.

 

“But don’t worry, I'll keep this under wraps until we have more concrete evidence. Then I'll let you know what I find out, and we can make a plan for our next steps.” 

 

Steve relaxed, and said sincerely, “I don’t think I could ever thank you enough for this Tony, but thank you again.” His gaze was so painfully sincere that Tony had to turn to the monitors so he didn’t have to see it. 

 

“No problem oh Captain my Captain. Now get out of here so I can be a genius.”