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 News

Phil exits the elevator and walks into the labs as that is where Jarvis told him Bruce would be. While Bruce is working on a computer near the elevator Tony is also in the lab working on a hologram of some piece of technology that Phil can’t understand. Both scientists look up when Phil enters the room.

“Hey Agent, how’s Skye?” Tony asks, turning back to his hologram.

“She’s alright, thanks for asking Tony. Jemma said she didn’t worsen any of her injuries with her power use when she woke up. She was in pain so Jemma gave her something for it and she fell back asleep. I’m pretty sure she will wake up again soon since that was over six hours ago. Actually that’s why I’m here. I was wondering what Skye can and should be eating. I don’t know when she ate last and she hasn’t asked for food yet but I’m sure she has to be hungry so can we give her something the next time she wakes up?” Phil asks Bruce.

“Well, we have been giving her nutrients through her IV since she was in desperate need of nutrition but yes, once she is awake and able to, it would be best to get some real food into her. With how much weight she has lost her body will not like large meals right now so several smaller meals throughout the day would be best for now. Also, since she no longer has a gallbladder, her body may have a harder time processing high fat meals. Basically, we need to start slow and light, some toast, applesauce, broth, Jell-O, things that are easily digestible, and work our way up from there.” Bruce says. Coulson nods along as Bruce speaks, starting a mental checklist of things he can make for her.

“I can do that. Thank you Bruce. Is there anything else we should be keeping an eye on or looking out for?” Coulson asks.

“Just watch her for signs of PTSD. I think it would be nearly impossible for her to come out of this experience without some form of it, but we need to figure out how it manifests for her. She has had two pretty intense flashbacks already but that could have been a temporary symptom as her brain adjusted to the knowledge that she was safe. Or the flashbacks could become more frequent as her brain tries to work through what it experienced. She shouldn’t be left alone for the next week or so until we can figure out how and if her PTSD is showing itself.” Bruce says sadly.

“Are you worried about her hurting herself?” Phil asks surprised, he hadn’t even considered that as a possibility.

“Not necessarily, but I am concerned about her powers and what they could do to her if they come out during flashbacks. We all saw the damage that they did to her when we rescued her, if she is trapped in a flashback and she feels threatened like she did then, they could come out just as violently and that concerns me greatly.” Bruce says solemnly. All three men in the room pause as the implication of that information sinks in. Eventually Tony breaks the silence.

“I’m working on something that I hope will help. With the data that the tower collected from when Skye used her powers after her nightmare I was able to figure out some things. It seems like the molecules in the room around her were vibrating at a higher frequency than normal. The same with the floor and then eventually the whole tower. Best guess, until we can get her to use her powers in the lab where we can run more tests, is that her powers somehow let her change the vibrational frequencies of atoms.” Tony says.

“So… how can you help her with that? It sounds like when she vibrated the atoms around her she also started to vibrate her own body apart.” Coulson says, he is trying to wrap his head around the idea of just how powerful Skye could be and how dangerous her powers could be for herself.

“Well, I am looking into making a pair of gauntlets that will help to cushion and direct the vibrations away from Skye’s body. Now they would only be helpful when she is wearing them so these would probably be something she would wear in the field but at least she could use her powers when she wants to without hurting herself.” Tony says.

“Hold on. She hasn’t even recovered yet and you are already talking about her using her powers in the field. I mean, we don’t know if she will even want to do that, she might want to leave this life behind after what happened and who could blame her if she did!” Coulson says, getting mad at Tony for trying to rush Skye through this and back to fighting so soon.

“I’m sorry Phil, I wasn’t trying to imply that Skye should rush to start using her powers in action. I don’t mean to assume that she will go back to being an agent or even an Avenger one day. It’s just… from what I know about her, from what all of you have told me about her over the last month, that girl is a fighter. I just don’t think that someone like her will let this stop her.” Tony says.

“Well maybe she should. She would be safer if she chooses to walk away from this life.” Phil says, looking down at the floor.

“We all would Phil. But, that’s not how any of us are made. And if there’s one thing I am sure of, it’s that Skye has been trained and mentored by you and Agent May and that means she has been taught not to give up. You both showed her how to be strong and fight for what’s right, you can’t stop her from doing that now that you are scared of her getting hurt again.” Bruce says.

“I know. I just can’t help but hope she will choose to leave.” Phil says.

“Any maybe she will. But if she doesn’t, I will make damn sure that she has all the gear that she needs to keep her as safe as possible when using her powers.” Tony says.

“Thanks, Tony.” Phil says.

“I’m not doing it for you Agent.” Tony says, turning back to work on the hologram and effectively putting an end to the touchy-feely conversation before he can get emotional himself. The truth is he is doing it for Skye, because no one should have to go through what she has and she deserves to feel safe after everything she’s been through. He is also preparing combat suits for the twins should they choose to stay and fight with the Avengers. It is the only thing he can do to keep his guilt from destroying him.

Bruce and Phil share a knowing look before shaking their heads at the stubborn billionaire’s back. As much as he tries to hide it, everyone in the tower knows how much this experience with Skye and the twins’ revelation about his legacy have been bothering him. It is clear to everyone that he is wrapping himself up in making things to protect everyone because that is the only way he can express how much he cares about them.

Phil thanks Bruce once again for his help with Skye before getting back into the elevator on his way back to the common area.

Line Break

Phil exits the elevator into the common room and finds it deserted, as he enters the kitchen he realizes that the clock on the microwave says 1am. He shakes his head, not having realized it was so late. Phil asks Jarvis to tell the two men down in the lab that he says to go to bed. Jarvis lets him know that he will relay the message but he doubts it will have any effect since neither of them sleep regular hours anyway. Phil thanks Jarvis regardless.

Phil decides that before he goes back into the med bay to check on everyone else he is going to make sure the kitchen is stocked with food for Skye for when she wakes up, if not he is going to run to the grocery store and get what he needs.

To his surprise he finds a full jar of applesauce unopened in the pantry, several loaves of bread in all different varieties, and all the broth and Jell-O flavors anyone could want. He shakes his head, wondering who bought all of this and when, when he hears someone entering the room behind him. He turns to see May coming out of the hallway leading to the med bay.

“Pepper bought all that stuff days ago. I asked Maria about it and she said Pepper stocked it all up when she realized Skye would need some light meals for a while.” May says with a smile after seeing what Phil is staring at. He shakes his head with a smile on his face.

“How did we get so lucky, to have people so wonderful around us? People who care as much about our girl as we do.” Phil asks, pulling Melinda into his chest and wrapping his arms around her.

“I don’t know… did you know that Maria and Pepper have been dealing with the UN for us? Having to explain our incursion into the arctic.” May says from where she has her head on his shoulder.

“Did you know that Tony is working on gauntlets to help Skye use her powers safely if she decides to go back in the field some day?” Phil responds.

“Our family is pretty incredible.” May says, tilting her head back to look up into Phil’s face. He smiles down at her.

Then he leans down, and she leans up, and they kiss.

It’s not a long kiss, or a passionate kiss, but one full of unspoken words and a lifetime of feelings.

As the two part they can’t help but smile at each other, feeling that finally, finally, their relationship has become what it always should have been. And with that thought, they kiss again. This time longer and more passionate, until they hear a throat clear behind them. The two break apart instantly and look up like deer in the headlights into the smirking faces of Natasha and Clint.

“Bout time you guys did that.” Natasha says, her smile growing wider as the blush on Phil’s face deepens.

“Yeah, I lost a lot of money waiting on you two to get together.” Clint says. Melinda recovers quickly, throwing a glare at Clint that would send most special ops running home crying.

“Sorry to disappoint you Barton. If you two wouldn’t mind keeping this to yourselves for the time being we would appreciate it.” May says, though it is clear she is not asking. Phil finally recovers from the shock too.

“Yeah, we need some time to figure things out before letting the rest of the team know. And Skye shouldn’t have to worry about us too, not when she needs to focus on healing.” Phil says.

“No problem, we can keep a secret. Just know that when you do tell her, and everyone else, it will be a relief and not a concern. Just like it is for us.” Natasha says.

“What she means to say is, we are happy for you guys!” Clint says with a massive smile on his face. All the years of feeling like the two people in front of him just needed to pull their heads out of their asses have finally paid off, he couldn’t be happier.

“Did you two need something?” May asks, eager to change the topic.

“No, we just wanted to let you guys know we are heading to bed, but Jarvis will get us if you need anything.” Clint says.

“You finally going to get some sleep?” Phil asks looking at Natasha.

“I’m not giving her any choice.” Clint says with a smile as he gives Natasha a playful shove toward the elevator.

“Sleep tight you two.” Phil says with a chuckle as he watches the two board the elevator and leave.

“You know she only lets him do that so he can feel like he is taking care of her, she would stay up if she wanted to.” May says with a smile of her own.

“Yeah I do, and so does Clint, but it works for them.” Phil says with a shake of his head.

“How long do you think it will be before we are the ones catching them kissing in the kitchen?” May asks.

“Not long at all… Are the others still asleep?” Phil asks.

“Yeah, they were when I left. Fitzsimmons are practically in each other’s laps, yet another couple that could get together any day now.” May says with a smile at Phil.

“Yeah well, in the meantime, Pepper was putting plates together for all of you when I left to go talk to Bruce and Tony so why don’t we have some food and then go rejoin them?” Phil says.

“Sounds good.” May says and the two start pulling out plates from the fridge. Since Pepper actually made four plates, one for Coulson too, they both reheat one for themselves and eat together before returning to the med bay. When they enter they see Fitzsimmons curled up together, now on a single chair, with their heads on each other’s shoulders. As the door closes behind May the two begin to stir.

“What time is it?” Fitz asks, rubbing his eyes as he subtly moves back to his own chair.

“Just after 2 in the morning. If you guys are hungry Pepper made you a couple plates of food. They are in the fridge ready to be reheated. If not, you should both go up to get some sleep in a real bed.” Phil says as he and May take their seats from before. Fitz stretches his arms up over his head as Jemma rolls her neck from side to side.

“Yeah, let me just check Skye over real quick and then we can go up to bed.” Jemma says. Fitz nods and moves his and Jemma’s chairs away from the bed so she has room to work. After a few minutes of checking vitals and bandages Jemma seems satisfied.

“When she wakes, if she is in pain, have Jarvis get me or Bruce.” Jemma says.

“Of course Jemma, you two go get some sleep.” May says and the two exhausted scientists trudge out of the room together. Once they are gone May and Phil take each other’s hands.

“What did Bruce say when you went to talk to him?” May asks after several minutes of silence have passed.

“He is worried about PTSD. He said that the two flashbacks that she has already had could’ve been the worst of it or things will continue to get worse as her brain processes what happened to her.” Phil says.

“We knew that already. Why do you seem so much more worried than before?” May asks.

“It’s just, hearing it from him, it sounded like he was worried about her hurting herself, and in a way he is. He is scared that if she keeps having flashbacks and they trigger her powers she will keep setting her recovery back or causing new injuries to herself. The only way I can think of to make sure that doesn’t happen is to help her learn to control her powers and use them properly, but when we brought that up before she seemed so terrified.” Phil explains.

“I know. I’ve been thinking about it too. We don’t know what Hydra was doing to her. Clearly whatever they did has caused her to be scared of her own abilities, we can’t get her to learn about them or control them until we can help her to realize that she doesn’t have to be scared of them, that we aren’t scared of them.” May says.

“It’s not fair. Cal and Whitehall said that Skye’s mother had powers too, she was special like Skye. Skye should’ve had her mother to teach her about her powers, to help her through this. But Whitehall took that from her. And now he took her father too.” Phil says.

“I know Phil, I know it’s not fair, we all know that nothing that has ever happened to Skye has been fair, but we can’t focus on that. We have to focus on helping her however we can. She may not have her parents but she has us, and we are going to do whatever we can to help her with her powers, even if we aren’t like her we can still help her.” May says, trying to convey a confidence that she isn’t entirely feeling.

“Of course you’re right. I’m just worried about her. I mean we haven’t even told her that Cal is dead yet.” Phil says.

“What?” A croak comes from the bed as Skye blinks her eyes open slowly. She had been slowly coming around to the murmuring voices in her room when those words broke through the fog in her brain.

“Cal’s dead?” Skye asks quietly.

“Skye… oh honey I didn’t know you were awake. I’m so sorry you had to find out this way but… yeah, Cal’s dead.” Phil says guilt pooling in his stomach.

“How? When?” Skye asks blinking back tears.

“It happened the first time that we tried to rescue you, when Hydra had all three of you still. You had been separated from Cal and Coulson. Do you remember that?” May asks carefully, she knows that that is when Whitehall forcibly gave Skye her powers and based on how Skye reacted the first time they spoke about her powers May assumes this will be a touchy subject.

“Yes.” Skye whispers, she doesn’t want to think about why she had been separated from them.

“When Agent Romanoff and I found Coulson and Cal they were frantic, trying to go after you. As soon as Romanoff had untied Cal he bolted for the stairs to the roof, we followed after him but by the time we made it to the roof Cal had been shot and the plane Whitehall had waiting was taking off with you on board.” May finishes, waiting to see how Skye reacts to the story.

“Was… did he suffer?” Skye asks, silent tears pouring down her face.

“No baby girl. It was very quick. He did say… he wanted me to tell you he was sorry. That he tried to protect you. And then he made me promise that I would save you. His last thoughts were of you.” Coulson says, tears slipping down his own face. Skye nods her head slowly.

“Are you alright Skye?” May asks after a few moments of Skye crying quietly to herself.

“Yeah. I mean it’s not like I knew him. He wasn’t in my life. It wasn’t his fault but he didn’t raise me so it’s not like I was attached to him or anything. He wasn’t really even my dad so why wouldn’t I be-“ Skye’s words cut off in a sob.

“Oh baby girl.” Coulson says as he climbs up onto the bed and pulls Skye against him, holding her as tight as he can without hurting her. Skye sobs against him, mourning the father she never got to know. The father who gave his life for her.

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