Theta Protocol

Marvel Cinematic Universe The Avengers (Marvel Movies) Agents of S.H.I.E.L.D. (TV)
G
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

Training

Wanda stood staring in at the poor girl asleep on the cot. No matter how hard she tried not to let the girl’s pain affect her, she couldn’t stop the wave of sympathy that rolled through her every time she laid eyes on her. With the sympathy came the rage at the men responsible for doing this to her.

With herself and Pietro it was different. Sure, they had been basically tortured by Strucker and List too, but they had volunteered. At some point they knew they were no longer allowed to leave and were now prisoners, not willing participants, but at least they knew how they had ended up here. They could blame themselves for the pain that had been inflicted on them. With this new girl, there was not one to blame but the men who had done this to her. Skye never wanted this, she didn’t ask to be treated like a lab rat.

And it was so much worse for her. With Wanda and Pietro Hydra knew where their powers came from, since Hydra were the ones to give them their powers. Sure they still performed some experiments on them to understand how their powers worked but it was never worse than some needles and scans. With Skye, Wanda shuddered at the visions in her mind of what Skye had been put through.

Ever since Skye had come out of the surgery Strucker had been dragging Wanda over to her cell to peer into her mind and tell him what she saw. Wanda was horrified with herself for digging through this girl’s deepest, darkest thoughts to find fears and insecurities, but she knew that if she didn’t cooperate then she and Pietro would be hurt. Besides, as long as Wanda kept relaying to Strucker how much pain Skye was in, he seemed to be alright with letting her stay on bed rest. It was the only way Wanda could think of to help her. She knew that as soon as Skye was well enough the next torture would begin.

Wanda had looked into Strucker’s mind too. She knew what he wanted. He wanted to figure out how to control Skye and her new powers, to use her as a weapon for Hydra. She had no idea how he would go about doing that, but she had no doubt it wouldn’t be good. The way that he smirked whenever Wanda told him about the terrible nightmares in Skye’s head told her that he was happy with her suffering. Wanda wasn’t deluded enough to think that Strucker would lessen her suffering once his training with her had started.

“What is going on in our little patient’s mind Wanda?” Strucker spoke from beside her, jolting her out of her thoughts.

Wanda peered into Skye’s mind and saw the same nightmare Skye had been having for weeks. She was being abandoned by her S.H.I.E.L.D. family, cocooned in rock, experimented on by Whitehall. There was so much pain. Wanda sucked in a breath, wishing she could help the girl but knowing there was nothing she could do.

“She is dreaming. The same nightmare as before. Reliving what Dr. Whitehall did to her. Going through the change again. She is in pain.” Wanda always left out the part about the S.H.I.E.L.D. agents. For some reason, she felt like it was too private to share with Strucker. She was sure he would find some way to use the fact that Skye saw the S.H.I.E.L.D. team as her family against her.

That was the one saving grace of this situation, Hydra couldn’t tell when Wanda was concealing things from them. Strucker smiled.

“It seems zat ze psychological torture of being awake during ze operation has proved more effective zan I could have ever predicted. I will have to commend Dr. Whitehall ze next time I see him. I have never been able to break someone down so effectively without physical violence before.” Strucker spoke without looking away from Skye’s body, twitching in her sleep. Her brows were furrowed and there were tears slipping down her cheeks.

Wanda shuddered, she hated that she had a part to play in this game that Hydra was playing with this girl’s life.

“How about when she is awake? What does she think about?” Strucker questioned Wanda. Wanda sighed, she knew she couldn’t evade the question.

“She thinks about S.H.I.E.L.D. and how she wants them to save her. She no longer fully believes that they will.” Wanda knew it was understatement. Skye was giving up hope. She didn’t believe that S.H.I.E.L.D. would save her anymore, not really. At first Skye spent all of her waking hours thinking about S.H.I.E.L.D., about what it would be like when they came to rescue her, about how they would take care of her when she got back home. Now, her thoughts just seem to spiral darker and darker every time she wakes up. She thinks about how they have probably moved on without her. How they are probably better off without her. She thinks that Coulson was the only person worth rescuing so now that they have she has been written off as a casualty of war.

“Hm… we will have to confirm zat for her zen won’t we.” Strucker said with a sadistic grin.

“Return to your cell Wanda. If you keep up this great work, perhaps you will earn some more freedom for you and your brother very soon.” Strucker said, glancing at her. He had promised that if she helped them with Skye he would consider allowing Wanda and Pietro to have free reign of the base, to be able to leave their cell whenever they pleased. So far that hadn’t happened, but Wanda wouldn’t give up.

Wanda turned around to walk away, shooting one last sad glance at Skye before she left. As much as she wanted to help the girl, she wouldn’t risk her brother’s safety for her. If helping Hydra get in Skye’s mind meant shifting Hydra’s focus away from herself and Pietro, she would keep doing it.

Line Break

Skye woke up with a start. The same damn nightmare scaring her into consciousness again. It has been getting worse. Now, instead of May and Coulson abandoning her the whole team is there in the dream. They are all telling her how much better off they are without her, how it’s a relief to not have to worry about what the troublesome hacker is doing. How they don’t miss her.

She has stopped listening to the voice in her head that tells her the nightmare wasn’t real. She is starting to think it must be true, or else they would have found her by now. They can’t be trying that hard to find her if they haven’t by now, so they must not be trying.

Skye sits up slowly, placing her feet on the ground. It no longer feels like her body is on fire when she breathes which is a small mercy. She is able to use her arms more since they removed her casts a few days ago. They still hurt, but much less than they did at first. The weird thing is that as the pain has lessened, the dread has increased. She knows that once Strucker determines that she is well enough, the next torment will begin.

Skye tries to mask the fact that she is feeling better. She stands up and hunches in on herself, hobbles over to the toilet in the corner, and winces as she sits down on it. She can feel their eyes on her at all times so she hopes that her pained expression will help buy her some time.

When she gets back to the bed, the door to her cell slams open. A man wearing a lab coat enters with two guards behind him. The guards hold their guns on Skye, daring her to try something. She doesn’t, resigned to her fate.

They have been doing this every few days, a doctor will come in, check the wounds on her stomach and change her bandages. The whole time at least two guards will hold her at gunpoint. She made a mistake one day, the doctor prodded at one of her larger incisions and pain flared through her. Before she could stop it, a tremor escaped her causing the entire room to shake. The guards both began screaming at her to make it stop, one of them slamming the butt of his rifle into her temple causing stars to explode in her eyes. She floated in and out of consciousness as the doctor finished his exam, one of the guards holding his gun to her temple the entire time.

Ever since then, she has been very careful about keeping the buzzing under control. She doesn’t know how to control the tremors without hurting her arms, but she does know that when she gets overly emotional or is in too much pain the tremors start. So, she resolves to keep her emotions in check as best as she can. When the doctor comes in this time, she doesn’t flinch or show fear. She simply raises her arms as the guards level their guns at her, and leans back to lay down on the bed, exposing herself for the exam, resigned to her fate.

Skye doesn’t see the gleeful expression on Strucker’s face as he watches from the window. He loves to see her give in so easily. Her will to fight back has almost entirely left her. As the doctor finishes his exam he turns to look at Strucker and gives him a nod, which makes Strucker’s smile widen even more. The doctor leaves the cell, but the guards stay, lowering their guns to allow Skye to sit up.

As Skye sits up, the pool of dread in her stomach spreads. Normally, the guards would leave when the doctor was done. Why did they stay?

“Congratulations Skye! Ze doctor has just informed me zat you’re healing incredibly well! So well in fact, zat he has given us ze go ahead to begin ze next part of your training.” Strucker’s voice caused Skye’s head to snap towards the glass. Her body began to shiver as he spoke, knowing that she was no longer fooling them with her act of pretending to be in more pain than she was.

“If you would like to follow me to ze gym, we can get started.” Strucker’s words may have sounded like a request, but the way that the guards raised their guns to point straight at her head reminded her that she had no choice. This time she didn’t have to fake the shaking in her legs as she stood. The fear was running up and down her spine, she felt the buzzing under her skin start to grow. She grit her teeth, forced herself to take a deep breath, and calmed down the tiniest bit. She knew she couldn’t let the tremors out now, not with the guards in the same room as her.

With a bit more confidence in her stride, Skye slowly moved out of the room. One of the guards dropped his gun in favor of tightly gripping her arm. Skye held back a gasp of pain as the guard tightened his grip on her still sore bicep. He took no notice of her discomfort though, instead he shoved her forward around the corner in front of her. They fell into step behind Strucker as he marched them along the labyrinth of corridors.

Strucker threw open a set of doors and Skye was thrust into a very large, open room. The concrete floors had pads covering it in an attempt to turn the space into a training room, but putting mats on top of concrete doesn’t do much to absorb the blow of a body being thrown to the floor Skye thought. She was proven correct when the guard holding her arm gave her a rough shove and she stumbled and fell, landing awkwardly on her knees, feeling the hard concrete under the worn down pad.

Skye slowly hauled herself back to her feet, Strucker’s eyes never leaving her body, his smile unwavering. She glanced around the room and realized that, on top of the two guards who had escorted her here and were now standing by the door they had come through, there were 6 more guards standing around the room. Her eyes went back to Strucker as he spoke.

“Well Agent Skye, let us see what your powers can do.” Strucker smiled at her. He pointed at a standing punching bag several feet away from them.

“Zat is your target. If you damage anything else zere will be consequences.” Strucker said.

Skye took a worried breath and looked at the punching bag. She had no idea how to control her powers. The only time she had let them out so far was when she was in pain or fear for her life. She didn’t know how to turn it on in an instant. She could feel the buzzing under her skin, but she had spent weeks pushing it down and suppressing it, now suddenly he expected her to use it. She looked at Strucker with wide eyes and gave him the tiniest shake of her head.

“I don’t know how.” Skye muttered out, no louder than a whisper.

“No time to learn like ze present.” Whitehall said. His words sounded light but his eyes had taken on a steely glint that reminded Skye just how much danger she was in.

She turned her gaze back to the punching bag. Slowly, Skye raised her right arm and aimed it at the bag. Nothing happened. She brought up her other arm and tried with both hands pointed at the bag. Still nothing happened. She looked back at Strucker. He was clenching his jaw so hard she almost thought she could hear something cracking. Skye closed her eyes and grit her teeth, willing something to happen. Still nothing did. She looked back at Strucker with tears in her eyes.

“I can’t.” She spoke.

“Skye, Skye, Skye, I was hoping to do zis ze easy way, but it seems ze only thing zat has worked so far is violence. We shall begin zere.” With his words, Strucker held up a hand and made a sweeping gesture to the guards assembled throughout the room. Instantly, they attacked.

Eight men suddenly ran full speed at Skye, kicking, punching, grabbing, she managed to block the first couple of blows but within an instant two of them had thrown her to the floor and suddenly they were all around her. They were kicking at every bit of her body. Skye had curled in on herself as soon as she hit the ground to protect the not fully healed incisions on her stomach.

Skye thought this must be it. If she couldn’t make something happen they were going to kill her, right here, right now. Well, maybe that wouldn’t be the worst thing. No one is coming to save her. She refuses to be Hydra’s lap dog. Maybe death is the only alternative.

Slowly, Skye stopped struggling. She released her grip on her legs and silently begged them to kick harder, if they were going to kill her at least they could make it fast. Skye felt the tremors building up inside her but she clamped it down, she would not make anything shake for them. They would have to kill her.

Suddenly, one of their boots found its way to her stomach. The hit to her incisions wrenched a scream from her throat and Skye was no longer able to stop the tremors. One slipped past her fingers causing the floor to rumble. Everyone froze, they all stopped their assault on her body. Skye caught her breath and tried to hold in the rest of the buzzing.

“Again!” Strucker’s voice rang out in the gym.

“No.” Skye muttered weakly. Strucker nodded at the man who had kicked her in the stomach and he leaned down and landed one, two, three hard punches to her stomach, then stood up and added two kicks for good measure. Skye screamed with each blow, the tremors escaping and increasing in intensity with every added hit. She felt blood trickling down her stomach and knew he had opened some stitches. She couldn’t focus on that though, because now that the tremors were loose, she couldn’t stop them.

The floor shook first, then the men gathered around her all started to lose their balance. Suddenly, the entire room was shaking, dust and chunks of rock falling down from the ceiling. They could hear muffled shouting through the door telling them the entire base was shaking too.

“Stop Skye! Now!” Strucker commanded.

“I can’t! I can’t make it stop!” Skye cried, screamed from where she was trembling on the floor. Whitehall strode up to her and put the barrel of his gun on her temple.

“Make it stop or die!” He said.

“Kill me! Please just kill me! I can’t control it!” Skye pleaded. She didn’t want to go on, not like this. She couldn’t control her powers, no matter how much they tried to make her, and she wouldn’t cooperate with them no matter what. She just wanted the pain to stop.

Whitehall snarled then he drew back his gun and brought it crashing into Skye’s head. She collapsed into a heap on the floor, the tremors stopping as soon as she was unconscious.

Strucker glared down at her limp form. He looked around at his men as they stood up from the floor, several of them having been knocked over by the force of the earthquake.

“Take her back to her cell, have ze doctor restitch her wounds.” The men all nodded, two of them took Skye’s arms and dragged her out of the room with the rest of them filing out behind them.

Strucker was at a loss. He couldn’t gain control of her powers if the girl herself didn’t know how to control them. He realized he needed a new plan, so he marched out of the room and headed for the labs.

Line Break

Striding into the lab Strucker saw scientists in lab coats scattered throughout the room, some of them were cleaning broken glass off the floor while others were gathering papers that had been strewn everywhere in the earthquake. His eyes landed on Whitehall and List on the other side of the room.

“Everyone out!” Strucker commanded to the room. Everyone snapped to attention, the scientists all hurriedly skittering from the room. Strucker slammed the door after the last man was gone and walked over to Whitehall and List.

“So, how’s our girl doing? It seems her powers are even stronger than I originally thought.” Dr. Whitehall said with a wide smile across his face.

“Strength is not ze issue doctor. Control is. She has no control over her powers. Ze only way to activate zem is pain and fear, ze only way to stop zem is to knock her out. I don’t want to waste my time teaching her to control zese powers, I want to use zem.” Strucker complained. He needed these two geniuses to help him come up with a way to gain control of the girl and her powers without killing her or his patience.

“With the twins, control was easy. As soon as they received their powers they seemed to understand how to control them. I had hoped the same would be true of the girl.” Dr. List added.

“Yes, but zeir powers were bestowed upon zem by us, ze girl’s powers were bestowed upon her by something beyond our understanding. Her powers are otherworldly. The twins powers came from ze scepter.” Strucker continued, feeling himself getting more and more frustrated. He heard a chuckle and looked over to see a smile growing on Whitehall’s face.

“What? What is it doctor?” List asked.

“The scepter. We can use the scepter.” Dr. Whitehall said, his glee rolling off of him in waves.

“We know the scepter is able to control minds. Even Barton was unable to resist its control. We can use it to control the girl and her powers.” Whitehall continued.

Strucker felt Whitehall’s elation spread to himself. They had never tried to use the staff for its mind control abilities, they hadn’t needed to. This was the perfect opportunity to test it, and if it worked, they would have a brand-new weapon in their arsenal. One who wouldn’t even think of disobeying because she wouldn’t have free will anymore. It was perfect.

Forward
Sign in to leave a review.