Theta Protocol

Marvel Cinematic Universe The Avengers (Marvel Movies) Agents of S.H.I.E.L.D. (TV)
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Theta Protocol
author
Summary
What if things went really bad in San Juan resulting in Skye and Coulson being taken by Whitehall, Skye being experimented on, and the Koenigs activating Theta Protocol. With Skye and Coulson missing and no leads on their location, team S.H.I.E.L.D. and the Avengers are going to need a miracle to find them before Dr. Whitehall is done with his experiment.Crossposted on FF.net
Note
Hi there. I have never written fan fiction before and I never really intended to but this little idea wouldn't leave me alone and I have been messing with it for about a year and it has turned into a pretty big idea so here we go. I would absolutely love any and all critiques, kudos, questions, encouragements, or ideas about ways to improve or things I should consider adding or changing. I hope somebody out there finds this idea as interesting as I do.
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Pain

It took a while for Skye and Fitzsimmons to release each other and for their tears to subside, but eventually Skye leaned back against the pillows that May had propped up for her while Fitz and Simmons each sat on a side of the bed. Coulson and May sitting in chairs on either side of the bed, watching the three fondly, immensely relieved to have them all back together again.

Skye looks exhausted, as soon as she slumped back onto the bed once her friends released her she let out a contented sigh and her eyes began to slip closed. Jemma really wished that she could let her go back to sleep but she really needs to ask her some questions first.

“Skye, I’m so sorry, I know you must be exhausted but I need you to stay awake, just a little longer. Can you do that for me?” Jemma asks, leaning down to push some of the hair out of Skye’s face. Skye’s eyes flutter back open and she gives a nod as she tries to refocus on Jemma.

“Good, just a few questions and a quick exam, then I promise you can sleep. First, how much pain are you in, scale of 1-10?” Jemma asks. Once Skye tells her how she is feeling, if she needs more pain meds, then Jemma doesn’t care if she sleeps through the rest of the exam. Instead of answering though, Skye gets a confused look on her face. The four people watching her all look at each other, hoping for answers, but no one is sure what is going on.

“Skye, can you tell me how much pain you are in? If you are in pain I will give you something for it.” Jemma says, hoping that if she explains why she is asking maybe that will help Skye answer the question. Still though, Skye doesn’t say anything, instead she looks down at herself, like she is taking stock of her injuries. Skye’s eyes scan over her body, her casted arms, wrapped ribs, the giant bandage covering her torso, and she looks even more confused.

“Skye, what’s going on? Do you understand what Simmons is saying?” Coulson asks after a minute has passed and Skye still hasn’t spoken.

“Yeah… yeah it’s just… I don’t know the answer.” Skye says, dropping her gaze so no one can see the tears forming in her eyes.

“What do you mean you don’t know the answer sweetie. How… how can you not know how much pain you are in? Are you not in pain? If that’s the case that’s a good thing. That means you are on the right meds, just say that and we- “Coulson keeps talking but Skye cuts him off.

“No, I’m… I think I’m in pain but… It’s the first time I have actually let myself think about it in so long. I… I have been in pain for days or weeks or… how long did they had me?” Skye finally looks up her eyes seeking out Coulson’s. Coulson can’t answer though, his throat is clogged with a sob that he is trying desperately to hold in. May answers.

“A little over a month Skye.” May says, Skye’s head turns to her and she nods slowly.

“A month… I tried not to think about it, tried not to focus on how much pain I was in the whole time. And now that I am thinking about it. I just don’t know what I’m feeling anymore.” Skye says slowly, tears dripping off her chin. May nods at her, realizing that she is the only one in the room capable of speaking right now she leans forward and gently cups Skye’s face in her hands.

“Ok. Well how about we do this together. How do your feet feel?” May asks, then she waits. Skye takes a long time as she turns her head to look at where her feet are hidden beneath the covers. Eventually she speaks.

“They are ok I think. Just a little sore. I… they never let me have socks or shoes and it was really cold so they have been numb for a long time. I don’t think I ever injured them though.” Skye says, turning back to look at May who gives her an encouraging smile.

“That’s good Skye, now what about your calves?” May asks. It doesn’t take Skye as long to answer this time.

“Same I think. Just a little sore. I don’t know why because I don’t think they were injured.” Skye says. Simmons seems to have recovered her voice finally so she chimes in.

“They are probably just sore from disuse and then being overworked during our rescue mission and when you woke up from your dream. Your body was thrown into fight or flight mode a lot and now it is coming down from that so your muscles will probably be a bit sore.” Jemma says with the most reassuring smile she can muster. Skye nods at her and then turns to look at her legs again, moving on without any prompting.

“My left knee is fine, just sore like everything else, but my right knee is in more pain. I think that the last time the guards beat me one of them might have kicked it.” Skye says, looking to Jemma for reassurance. It takes all of Jemma’s willpower not to breakdown at how easily Skye talks about being beaten but instead she nods and gestures at Skye to continue.

“My thighs are sore too, and they feel like they are maybe bruised or something. That’s probably from the beating too. Then something really hurts in my, um…” Skye trails off and Jemma supplies the words for her.

“Your groin. You have a cut there that we had to restitch. It looks like a lymph node was removed.” Jemma says, hoping that if she speaks clinically it will not be as traumatic. It seems like the right move as Skye just nods and keeps moving up her body.

“My torso is on fire. I know… I know Whitehall took a lot of stuff out of me. I had been doing better for a while but now it feels more like it did just after it happened.” Skye says and she looks confused by it. Remembering Coulson’s warning about Skye reacting badly to them talking about her powers Jemma decides to skirt around the topic for now.

“Yes, several of your wounds seem to have opened up during our escape, we had to perform surgery once we were safely back on the Bus and then again once we got here. You will be sore for a while but we will keep you on pain meds to help keep your pain to a minimum, how are your ribs?” Jemma asks, hoping to keep Skye moving forward and not dwell on how her injuries were reopened. She just needs Skye to get through this so she can give her more pain meds then let her sleep.

“They ache, when I take a deep breath the pain is worse but, it’s nothing compared to the surgery. My arms hurt too. And my shoulders hurt. My face hurts from where they punched me. My head hurts. I just… everything hurts. It has hurt for so long. I have hurt for so long. I’m tired of hurting May.” Now that she is thinking about it, the pain is overwhelming. Skye leans over and May immediately stands up and takes her into her arms, once again sitting on the bed to let Skye rest against her.

Fitz stands to make room for May on the bed, moving to stand behind Simmons. Jemma turns away from the scene unfolding in front of her and buries her face in his stomach as she lets out the tears that she has been holding back since Skye started talking. He tries to ignore his own tears as they slide off his face.

Coulson moves in to place a hand on Skye’s head, tucking her hair behind her ear as her sobs subside. Skye turns her head just enough to look at him, not withdrawing from May’s protective embrace.

“I’m so sorry baby girl. So sorry that you have been in this much pain for so long, but you don’t have to be anymore. You did such a good job Skye, telling us what you are feeling and what is going on with you. Now that we know we can help you, right Jemma?” Coulson turns to look at the foot of the bed where Simmons has pulled herself to a standing position and she plasters her most encouraging smile on her face as she nods at Skye before moving away to get the pain meds together, Fitz following behind to help in any way he can.

“I know it must seem impossible right now baby girl but you are going to get through this. We are going to help you through this, all of us. You will never be alone again, we will never let you deal with any of this by yourself. You just have to keep talking to us, keep telling us what you are feeling, and let us help you.” Coulson says and Skye gives an almost imperceptible nod.

“Skye, I’m going to give you some more pain medication through your IV, you should start to feel better really quickly. If you get sleepy just give in to it alright. I need to check your stitches and run some tests to make sure everything is healing how it should but you can sleep through it ok.” Jemma says as she starts to push the meds into the IV bag. Skye turns her gaze to Jemma’s and then to Fitz’s, finally looking back at Coulson as her body begins to feel like it is floating. Her eyelids begin to flutter as Coulson leans down to press a kiss to her head, May continuing to stroke her hair, as Skye slips into unconsciousness.

Line Break

No one says anything for a long time after Skye falls asleep. Fitzsimmons and Coulson just stand around the bed watching her sleep while May holds her close, stroking her hair.

None of them were under any illusions about how difficult this would be. They all knew that Skye was going to be traumatized from this experience and that she had been through things that no one should ever have to go through but hearing it firsthand is another thing entirely.

None of them were prepared to have to listen to her describe the amount of pain she had been in for so long without any hope of doing anything about it. No one should ever have to be in pain for so long that they stop thinking about it. Skye didn’t even seem to know what her own body was feeling anymore, she had just stopped paying attention to it. It was the only way she could survive.

“Can she ever come back from this?” Fitz asks after no one has spoken for ten minutes, everyone just watching Skye sleep.

“We all have to be patient, we have to be ready to support her through it. She is going to go through a lot. The emotional recovery from this will be so much harder than the physical. It will likely get worse before it gets better. We all have to be ready for that.” Coulson says sadly. The room falls quiet once again.

“We will get her through this. Together.” May says from the bed where she hasn’t stopped stroking Skye’s hair and face since she fell asleep.

“Alright, I still need to give her an exam. We will need some privacy, if you would all please wait outside for ten minutes or so.” Jemma says after a while, once everyone has regained their composure. Fitz and Coulson begin to move toward the doors right away, but May makes no effort to move.

“May.” Jemma says, then she looks to Coulson for help.

“Melinda, we need to let Simmons work.” Coulson says. May ever so gently gets up from the bed, being careful not to jostle Skye as she does, but instead of moving towards the door she sits in one of the chairs.

“I am not leaving. I won’t get in your way Jemma but I’m not leaving her alone. If she wakes up and Coulson or I aren’t here I don’t know what will happen. I won’t take that chance.” May says firmly. Coulson looks to Jemma who nods and shoos the two men out of the room.

“This may not be pleasant for you to see.” Jemma says as she begins to undo the bandages around Skye’s torso.

“It’s not pleasant for you to see either Jemma. Skye is not the only one that I refuse to let go through this alone.” May says, catching Jemma’s gaze for a moment before she returns to her work, feeling reassured by May’s presence instead of encumbered by it.

As Simmons carefully examines all of Skye stitches, performs scans on her arms, and changes out her IV bags, May sits or stands silently, guarding the two. She moves out of the way whenever Jemma needs her to, but she always returns right back to her seat as soon as she can.

At one point, when Jemma began to press on her stomach, Skye started to show signs of stirring. She jerked away from Jemma’s hands and her eyelids began to flutter open. May swooped in, grabbing Skye’s hand and whispering reassurances in her ear while Jemma finished that part of her exam. May didn’t stop until Jemma had rebandaged her.

Eventually, Jemma finished. Having examined, cleaned, and redressed all of Skye’s wounds and taken all the necessary scans, uploading everything for Bruce to review. When she was done Jemma went to the door to let Fitz and Coulson back in and informed the small group that Skye’s power usage had not done any damage this time.

With that reassurance the team took up positions around Skye’s bed, pulling up two more chairs for Jemma and Fitz to sit in. That is how Natasha and Clint found them two hours later, May and Coulson on one side of the bed, Fitz and Simmons on the other, all asleep with their heads or hands resting on Skye’s bed.

Line Break

It wasn’t until much later that day that any of them woke up, Coulson stirring from where he had fallen asleep with his head in one of his hands and his other hand on top of Skye’s. He straightens up in his chair and stretches out, feeling the strain from having slept for so long in an awkward position. As he looks around the room he is reminded why.

Next to him, May is asleep with her head on the bed and her hand on Skye’s leg, across from them Fitzsimmons fell asleep with their heads pressed together and their hands on Skye’s other hand. Coulson can’t help the smile that creeps onto his face, looking at his team, all back together again. With one last look he decides to leave them all to their much needed rest and venture out to check on the rest of the occupants of the tower.

In the common area he finds the rest of his agents, Mack, Tripp, Bobbi, and Hunter, all sitting on the couches and chairs. The four stand and hurry toward him the second they notice he has entered the room.

“How is she sir? Barton and Romanoff went in a few hours ago to check on you all since you had been gone for so long and they said you were all asleep.” Bobbi asks.

“She is ok, or at least as ok as she can be after what she’s been through. It is going to be a long road, I think we all know that, but she knows we are here to help her. Once we got her to tell us how much pain she was in Jemma upped her meds and she fell back asleep for the rest of the exam. I guess we all needed some sleep too cuz once the exam was done we all passed out.” Coulson says. Looking around at the worried faces of his team he is reminded once again that the four people in the med bay are not the only members of the extended family that they have made for themselves over the past few years.

“I know you all want to see her for yourselves, next time that she is awake we will ask her if she is ready for more visitors. I’m sure she will want to see you guys too, she just might need a bit more time before she is ready for that.” Coulson says.

“Of course, sir. I don’t think any of us care about how long it takes. We are just happy she is doing well.” Tripp says in his usual comfortingly upbeat manner. Coulson claps him on the back, smiling at his agents.

“I know I don’t say it enough, but I am so grateful that you all are a part of this team. I just hope you all know that.” Coulson says, fighting the tears in his eyes. Sleep deprivation and his relief at having Skye back are making him real mushy right now but he can’t find it in him to regret it when he sees the blushing, smiling faces looking back at him.

“Don’t go soft on us Director.” Mack says with a smirk on his face while Bobbi punches his shoulder.

“I agree, this isn’t a Hallmark movie Coulson.” Hunter says with a shit eating grin as he dodges the punch that Bobbi throws his way. Coulson shakes his head at their antics and leaves the four squabbling agents behind as he heads for the kitchen.

“And here I thought Tony was the childish one, watching those four rough house, I think they might give him a run for his money.” Pepper says, standing by the stove with a cup of tea in her hands.

“Yeah well, you take a bunch of highly trained operatives and put them together in a room for too long without an assignment, stuff happens I guess.” Coulson says, moving to the fridge to take out some leftovers, intending on reheating some food for May and Fitzsimmons for when they wake up.

“Do you need help?” Pepper asks.

“That would be great, thanks Pepper. I just want to put some plates together for May and Fitzsimmons. I don’t know when they will wake up but they will probably be hungry by then.” Phil says as Pepper starts to help him with the food.

“What about Skye?” Pepper asks and Coulson stops what he is doing for a second, then he shakes his head at himself.

“I don’t know. I don’t know what she is allowed to eat right now. She… she has lost a lot of weight. I want to get some food into her, help her start getting it back but… Bruce said how much weight she has lost in such a short period of time means that she is technically malnourished I mean, how do I help her with that? How have I not thought about this sooner? I need to talk to Bruce, figure out what I should be doing. I can’t believe I didn’t think about this. I failed her again!” Coulson rambles, getting more and more frantic as he goes. Finally, Pepper reaches out and roughly grabs him by the shoulders.

“Phil! Breathe, Phil. This is not your fault. You cannot do everything, be everything all at once. You are doing the best that you can, all of you are. You didn’t think of this sooner, but neither has anyone else. Skye hasn’t been awake long enough to be fed yet anyway so it hasn’t been an issue. Now that you know, you are right. We can talk to Bruce about what to do next and how to help her best, but breaking down won’t help her. Ok?” Pepper says, forcing Coulson to look at her as she speaks.

“Ok. You’re right. Of course you’re right. Thank you Pepper. I just-“ Pepper cuts him off.

“You are a worried father.” Pepper says with a smile.

“No… I’m not Skye’s father.” Coulson says, though honestly he is wondering who he is trying to fool.

“Right… well how about I take care of this while you go talk to Bruce?” Pepper says knowing that now isn’t the time to push him on this topic, not when he is already so overwhelmed.

“Yeah, thanks Pepper. If May or Fitzsimmons come out before I come back please let them know what we talked about.” Coulson says before shuffling off to the elevator. Pepper smiles after him, shaking her head.

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