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.
All Chapters Forward

The Vow

Everyone is still gathered in the common room six hours after the doctors came out. Bruce helped himself to some food and then joined the rest of the group in the long wait for Skye to wake up. Dr. Cho’s team left a couple of hours ago, leaving Skye’s care in Bruce and Jemma’s capable hands now that she is stabilized. They are under strict orders to call Dr. Cho with an update when Skye wakes up.

Bruce and Jemma have each gone in a couple of times every hour to check on their patient but there has been no change in her condition. She is no longer under sedation but she is on some pretty strong pain meds that have their own sedating effects, so they aren’t too concerned that she hasn’t woken up yet. Every time they go into the room May and Coulson look expectantly at the two doctors, hoping for good news. Every time they hear that there is no change and they have no way to predict when Skye will wake up, the pair sink further into their seats.

They have each had to leave the room a couple of times to go to the restroom, making the trip as quick as possible each time, trusting the other not to leave Skye alone while they are gone. They are sitting on different sides of Skye’s bed and each have one of Skye’s hands in theirs. Her bruised fingers sticking out of the ends of the casts on her arms acting like anchors for the two. Even with the exhaustion they feel, they both refuse to sleep, to eat, to do anything that will distract them from their vigil over their girl. They are watching her so intently that they both notice the moment that Skye’s eyes shift under her lids.

Line Break

Most of the group is asleep. Thor is sprawled across an armchair that he doesn’t fully fit in. Fitzsimmons are curled up next to each other on a couch, needing each other’s comfort even in sleep. Hunter and Clint have their heads tipped back on another couch while Bobbi sleeps with her head in Hunter’s lap and her feet in Clint’s. Tripp, Mack, and Tony each claimed an armchair as well. The twins have squeezed themselves into a chair that should only fit one, but somehow they still seem remarkably comfortable. Pepper and Maria have both dozed off on top of their open laptops. They were doing damage control with the government, explaining the Avengers presence in the Arctic, and eventually the snores of the others had lulled them both to sleep as well. Bruce is in the same position as the two women expect he fell asleep on top of the tablet from which he is monitoring Skye’s vitals.

Natasha and Steve are the only ones still awake, watching over the group of Agents and Avengers. Steve tried to quietly tell Natasha to get some rest but she shut him down with a look. He understood. She won’t sleep for the same reason he won’t. Not until Skye is awake. Not until Coulson and May are ok. Not until the team is whole again.

The only sound in the room is the various breathing from the sleeping bodies. Some loud snores occasionally escape Thor or Mack, but otherwise the room is rather quiet. Steve and Natasha immediately notice as worried muttering from Wanda breaks the silence.

Both of their heads snap to the girl’s sleeping form. Her body, which had been still up till now, is currently twitching and there is a tiny tendril of red swirling around the fingers of her right hand. Steve jumps up and hurries over to the girl but before he can make it there her movements wake her brother who is pressed up against her.

Pietro’s eyes immediately search for a threat, landing on Steve who is rapidly approaching. Steve freezes in his tracks, holding up his hands to show that he means no harm to the pair. Pietro stares at him for a moment until he feels his sister move against his side and he turns to see her still muttering and squirming about.

“Wanda, wake up. It’s just a nightmare. Wanda!” Pietro tries to rouse her, quietly at first, but she doesn’t respond. He shakes her gently but she still doesn’t wake. The power around her fingertips begins to grow and Pietro knows he can’t waste time with politeness. The last thing they need right now is for Wanda to accidentally lose control of her powers and hurt someone in this group. They may not have locked them up yet but they surely would if Wanda injured one of them.

“Wanda! Get up! You are having a nightmare! It isn’t real! Wake up!” Pietro begins to yell at his sister, shaking her roughly. The Avengers and Agents around the room all wake up, most of them jumping to their feet looking for a fight. They freeze when their eyes land on the scene unfolding in the middle of the room.

Suddenly, Wanda awakes with a scream. Her eyes fly open, the red color of her irises matching the red that is slowly spreading across the room. She looks around frantically before her eyes lock on Pietro’s. She forces herself to take a deep breath as she pulls her power back into herself, Pietro holding tight to her hands as she grounds herself in his presence. Finally, after Wanda seems to have regained her composure and calmed down, Pietro speaks.

“It was just a nightmare.” Pietro says. Wanda begins to nod. She thinks back to her nightmare, trying to understand it, when a realization dawns on her and she freezes. It wasn’t a nightmare, they were memories. And they weren’t her memories.

“No, it’s Skye.” And before anyone can stop her, Wands runs from the room, her brother and the entirety of both teams right behind her. Wanda bursts into the room. Skye is awake, her eyes are open, but they are unseeing. She has pushed herself up against the headboard of the bed and she is trying to make herself as small as possible, pulling her legs to her chest as if she could disappear behind them. She is stuck in a flashback.

May and Coulson’s heads snap to the door when it slams open and everyone rushes into the room. May throws her hand up and they all freeze. May and Coulson have stepped back to give Skye a bit of space and they both have their hands held out in front of them, like you would to calm a frightened animal.

Nobody moves or speaks as they all watch, wanting to help but knowing they can’t. May slowly creeps back towards Skye, her eyes never wavering from Skye’s even though it is obvious the girl is not seeing her. May starts calmly speaking to her.

“Skye, Skye it’s me, it’s May. You’re safe now. (No response) Can you hear me. (No response) Just breathe Skye (Skye breathes), you’re safe.” May pauses to give Skye a moment to come out of it, when nothing changes, Coulson tries.

“Skye, can you look at me? (No response) C’mon sweetheart. (No response) Look at me Skye (Skye looks at him, her eyes still unseeing.) That’s good. You just had surgery Skye, you really need to lay back down so you don’t rip your stitches out. Can you do that? (No response) Please Skye, lay back down (Skye lays down.)”

“Stop.” Clint says suddenly from the back of the room. Everyone’s heads turn to look at him. May is ready to snap at him for interrupting and tell them all to get the hell out when she sees Clint’s face. He is white as a sheet. He is looking at Skye like he has seen a ghost. May goes from angry to concerned in an instant.

“She is only responding when your words are phrased like commands, not questions. She thinks she is still under the effects of the staff. You have to stop telling her what to do until she is in control again.” Clint seems like he is having a hard time getting the words out and everyone knows why. He is clearly remembering exactly what it was like when he was under the staff’s effects.

“He is right. When they used the staff on her they gave her one directive. Obey. That is all that is going through her mind right now. She thinks she must obey.” Wanda says. The others clearly seem uneasy with the fact that Wanda seems to be able to read Skye’s mind but they will put that aside for now. Right now they just need to help Skye.

“So, what do we do? Can you help her?” May asks.

“I don’t think so. My powers… I can plant thoughts in her head, but they would be false. I was able to free her from the mind control of the staff because that was an external force invading her mind. This is not, this is internal, coming from herself. This is…” Wanda trails off, unsure of the word for this.

“Trauma.” Natasha finishes for her. She knows all too well what it is like to have your mind taken over by memories of your past. She wishes she knew how to stop it, but even with all her experience she still doesn’t.

The room exhales collectively. There is not a single person here who has not dealt with trauma in some form or another. They all feel a wave of sympathy for what Skye is going through.

“Bruce, Jemma, any ideas?” Coulson asks. He is finding it more and more difficult to look at Skye. She laid down when he told her to, but her body has not lost any of the tension that it had before. Her eyes are still open, staring at the ceiling. She seems oblivious to the conversation going on around her.

“I need to check her stitches, make sure she hasn’t torn anything. Even if she isn’t consciously aware of it she must be in considerable pain. The only thing I can think is to sedate her so I can examine her and hope that maybe the next time she wakes up she will be more lucid.” Bruce says after a moment. He doesn’t like the idea of putting the girl out again so soon after waking up, but he really doesn’t like the idea of doing an exam on a conscious patient who is not able to give consent and who will take any of his statements as commands that she must follow.

“Jemma?” May asks, needing to hear what she thinks before she agrees to this.

“I… I think Bruce is right. We can’t help her like this.” Jemma says, tearing her gaze off of her sister in the bed. May and Coulson share a long look where they have an entire conversation without words before Coulson nods.

“Do it.” He says. Bruce and Jemma move forward to prepare the sedative. May and Coulson move to one side of the bed and both lean over to take Skye’s hand as Bruce plunges the sedative in the IV. After a moment Skye’s eyes flutter close and the tension finally bleeds out of her body. The entire room seems to heave a sigh of relief.

“We need some privacy while we examine her stitches.” Bruce says after a moment when no one seems inclined to leave. His words seem to snap everyone out of their trance and they all shuffle out of the door. May and Coulson are the last to go, glancing back at Skye one last time before allowing the door to close softly behind them.

Line Break

When they get outside the room everyone turns to head back to the common room, except May, who turns and marches quickly down the hallway in the other direction.

Once out of sight of the others May breaks into a near sprint, turning corner after corner, no idea where she is going, until she ends up at a dead end. With nowhere else to go, she slams both her hands on the wall in front of her and breaks.

Melinda May breaks.

Breaks in a way that she hasn’t in years. Not since Bahrain, since the last time that she dealt with someone who wasn’t in control of their own mind. A poor little girl, with powers she didn’t understand, who was confused and scared. Someone the world had hurt and thrown away. Someone just like her Skye.

All of the pain, the worry, the relief, the fear, the dread, the hope, and the heartbreak that May has felt since Raina showed up at the base comes pouring out of her as she pounds her fists on the walls, making sounds she didn’t know she could make.

She slides down the wall, landing gracelessly on the floor, and turns to see Coulson standing a few feet away. He doesn’t say anything, doesn’t approach, he just stands by and waits, turned so that he can see her out of the corner of his eye if she needs him but also able to watch the hall in case someone tries to approach.

She sits on the floor with her back against the wall and cries for what feels like hours but is probably only minutes until she slowly starts to get her breathing under control.

Eventually, once the worst of it has passed, Coulson moves in and sits beside her, far enough way for her to dictate how much space she wants, but close enough to provide the support that she needs.

After a few more minutes May reaches her hand out to him and Coulson takes it as an invitation so he slides over and puts his arm around her. Instantly, May collapses against him, her head on his shoulder, her arms slung around his waist, absorbing the steadiness he provides. Finally, she talks.

“I can’t do this Phil. I’m not strong enough, not good enough, to get her through this. What she went through… she is broken Phil, and I’m too broken to fix her.” Melinda cries against his shoulder as her confession passes her lips. Coulson just pulls her tighter to his side as he speaks.

“You are the strongest, most capable, most good person that I know Melinda May. I don’t care if you think you are broken, I don’t care if you think you aren’t the right person for this. I’m telling you that you are the best, the only person who can help our girl Melinda. All the things that you think make you unworthy or broken are the exact things that are going to help her now. You can understand what she has been through, what she is feeling, in a way that no one else can Melinda. You are not broken, and neither is she. She is hurt, and we will help her heal.”

“What if I can’t. If I fail, we could lose her Phil. I can’t lose her!” Melinda feels more tears escape as she finally says the words out loud that she has been thinking since Skye was first taken.

“You don’t have to do it alone, any of it. We will do this together. And we have a whole team, a family here who wants to help her too. She will never have to go through any of it alone. None of us will. We have to let them help us so that we can help her.” Coulson says. He knows they have been acting stupid the last 24 hours, so focused on Skye that they have been shutting everyone else out. They need their family now more than ever. He is not going to keep making the same mistake. He feels Melinda nodding against him.

“I’m scared Phil.” May practically whispers.

“I know Mel, me too. But we can do this. We have to do this, for Skye.” He says.

The two of them stay there for a while longer, regaining their composure and recovering from the shock of Skye’s flashback until Phil’s stomach lets out a massive growl and neither of them can stop the small laughs that escape them. Coulson stands up and reaches out a hand to pull May up. With one last cleansing breath the two make their way back towards the common room to rejoin their family.

Line Break

When May and Coulson walk into the common room no one mentions the obvious puffiness of May’s eyes or the wet spot on Coulson’s shoulder. The group has returned more or less to the places they were before they were abruptly woken up, though now that Skye has woken, even if it was a rather terrible first awakening, the mood has lightened considerably.

With a glance around the room May and Coulson spot the pile of now cold food and move over to pick through what is left, too hungry to worry about heating anything up. All the eyes in the room follow them and everyone breathes a sigh of relief when they see the two eating. After a moment of silence with everyone just relishing in the fact that things have improved, at least a little bit, Bruce comes out from the med bay.

“She’s doing well. Somehow, she managed not to tear any of her new stitches, I credit Dr. Cho and her team for their work. I called her and updated her on Skye’s condition. She is pleased with her progress. Skye will be unconscious for at least another 6 hours. Jemma offered to sit with her so you both could take a break.” Bruce finishes, addressing Coulson and May who look at each other and, remembering their conversation, share a nod.

“That sounds good. Thank you, Bruce.” Phil says as he and May each move to sit on one of the couches.

“I’m going to go join Simmons.” Fitz says and he gets up and leaves the room to no one’s surprise.

The room falls quiet again, there are a few hushed conversations occurring but mostly everyone is just enjoying the feeling of rightness that is passing through the room. After weeks, months of searching for Skye she is finally safe. She may not be well yet, but there is the hopeful feeling that she is going to be. And now that May and Coulson have begun to take care of themselves again the group feels the tension bleeding away.

Now that May and Coulson have eaten and begun to feel more like themselves, their eyes fall on the two new editions to the room. They both feel like they must have missed something. The last time that they saw the twins they were standing together, apart from the group, looking uncomfortable and suspicious of everyone. Now, they are sitting together on one large armchair in the middle of the room full of Avengers and Agents and while they don’t look completely at ease, they are much more relaxed than before. Wanda has a soft smile on her face while Pietro seems to be enjoying listening in to the bantering conversation going on between Mack and Hunter. Not to mention that Natasha is no longer watching them suspiciously like she was before which is a huge vote of confidence from the paranoid spy.

“We haven’t had a chance to thank you two yet. For helping us get Skye away from Hydra. For freeing her of the staff’s control.” Coulson says. All eyes fall to the twins. Wanda’s cheeks take on a deep blush and Pietro turns his gaze to the floor.

“We may not have been able to get her out of there if you hadn’t done what you did Wanda, thank you.” Coulson continues and May nods her head. Even as the blush on her cheeks deepens, Wanda feels her eyes drawn to Coulson’s. There is genuine warmth and gratitude in them. She doesn’t know what to do with it.

“Skye didn’t deserve what they did to her, what they would keep doing to her. I am sorry we could not help her sooner.” Wanda says, feeling guilt well up inside of her. All those times she was forced to look into Skye’s head and she saw that the girl was giving up, losing faith that S.H.I.E.L.D. would come for her. Wanda wishes she could have helped Skye before she lost that hope. Now that Wanda is here, surrounded by them, she can see that they would never have given up on her, no matter how long it took.

“She never stopped dreaming about you. Even after she began to lose hope that you would find her, her mind still told her you would come.” It’s not fully true. Most of Skye’s dreams ended in her being abandoned by the team. But for some reason Wanda finds herself wanting to comfort the two people staring at her with so much gratitude.

“How do you know she dreamed about us?” May asks. Wanda looks down, shame creeping up her spine. She feels Pietro grasp her hand.

“My powers. I was able to conceal some things from Hydra, like the fact that I can control minds, but they knew that I could see people’s thoughts and plant new ones if I wanted.” Wanda swallows hard, her mouth suddenly feeling very dry at the prospect of having to reveal how she violated Skye in the most intimate way possible.

“After Skye had been brought to the facility where Pietro and I were being held, Strucker would make me look into her mind to tell him what she was thinking, what she was dreaming. I did not want to do it, I swear. I never wanted to use my powers on Skye. But I was afraid of what he would do to Pietro and I if I didn’t. After the surgery Skye dreamt of what they did to her every night. Sometimes in her dreams you would come to save her. Eventually, in the dreams, you stopped coming to save her, but she still dreamt about you. She dreamt of good memories she had with all of you.” There is silence for a long time when Wanda stops talking. Finally, she forces herself to look up and sees that the two agents both have tears running down their faces.

Wanda can’t fight the tears that force their way out of her eyes too. She wishes she hadn’t told them that, all it did was hurt them to know that. She looks down at her hands where they have entwined with her brother’s.

“I’m so sorry.” Wanda mutters weakly.

“It’s not your fault Wanda. You did what you could. Once you saw a chance to help her, you took it. It’s the only thing you could have done in that circumstance. I’m sorry we couldn’t get you guys out sooner.” Coulson says as tears continue to pour down his face.

Wanda can’t believe what she is hearing, is he really apologizing to her. Apologizing for not saving them from the mess they got themselves into. They volunteered. The pain that they suffered was their own fault. It is not his fault. Wanda doesn’t know what to say so she just nods and sits back in the chair hoping that she won’t be required to speak anymore. She needs time to think and from the look on Pietro’s face so does he.

Coulson and May seem just as inclined to let the topic drop so the others slowly pick up their conversations again. All letting the devastated pair process what they had just heard.

All that Coulson and May can think about is how much they let their girl down. They promised to save her, they promised to protect her, they promised that they would never abandon her, but they failed. They didn’t keep their promises. Her whole life, every family that Skye ever had abandoned her and here they were doing the exact same thing.

Wordlessly, the two grab each other’s hands and make a new vow to their girl, one that they would die before breaking. They are going to get her through this, they are going to do whatever it takes to help her get better. And they are never going to abandon her ever again.

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