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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The Plan

Coulson and May returned to his office to a flutter of activity and conversation. Clint, Natasha, Tony, Steve, Bruce, Bobbi, Tripp, Hunter, and Mack were in a semi-circle around the projector screen discussing strategy. Clint and Hunter seemed to be arguing about the best way to get into the facility. Fitzsimmons were sitting very close together, staring at his computer screen. It was obvious from their posture that they were listening intently to everything that was being said but they were not contributing. They were the only ones to notice Coulson and May enter the room.

As soon as they saw them, they both stood up and hurried over to them. It was something that had been happening a lot lately. The four of them, the OG team as Skye liked to call them, had been gravitating toward each other a lot, seeking comfort from each other in Skye’s absence. In this particular moment, they needed a second, just them, to share in the hope that they might make their family whole very soon. After a few seconds of silence and a deep breath shared between them, Coulson nodded and turned to the rest of the room.

“Alright!” Coulson’s voice boomed across the room, silencing the heated discussions that were going on. Every head turned to look at him as he moved to stand at his desk, May coming to stand beside him, Fitzsimmons going to stand by his computer.

“What do we know about where she’s being held?” Coulson asked. The others all shifted, looking at each other, wondering who would speak up. Jarvis decided he would step up if no one else would.

“Sir, it seems Raina was being truthful. We located a large structure in the Arctic right where she said we would. The scans that I have run show dozens of people inside. They have fully operational missile defense systems. The team were discussing how to get close without being detected when you returned.” Jarvis supplied with no small amount of sass in his voice.

“There is nothing around for miles, they will see us coming, with or without cloaking, and blow us out of the sky before we can hit the ground.” Clint added.

“Which is why we should blow the missiles before we try to land. It’s the safest option.” Hunter piped up, looking at Clint.

“If we do that they will know we are coming and they could kill Skye, and any other hostages they might be holding.” Bobbi came to Clint’s defense, much to Hunter’s irritation. The room fell silent again, everyone thinking of an option that would get them there but wouldn’t get Skye killed in the process.

“Ideas people? We can’t just sit here twiddling our thumbs while Skye is fighting for her life! Tony, you got anything that could help us?” Coulson asked after no one had said anything for several minutes. He didn’t want to waste time standing around his office when they should already be on their way to Skye.

“The only thing I could suggest is using my Iron Legion. I have two dozen iron man suits that can operate independently. I could program them to each destroy one of their missile deployment systems simultaneously, allowing us to fly in and land right away. It is the fastest option. I can’t guarantee that they won’t kill Skye once they know that we are coming, but if we do it that way we could be on the ground within five minutes of the first point of contact. Hopefully we could get to her quick enough that they won’t have time to hurt her.” Tony said.
“I still don’t like it. Once the first hit happens Hydra could take her out immediately.” May said, she didn’t want to do anything to risk letting Hydra know they were coming.

“Sir, something is happening. Raina.” Simmons spoke suddenly from the side of the room where she was watching Fitz’s computer. She put the feed into Raina’s cell up onto the wall for everyone to see. Raina was frantically waving her arms at the camera and saying something. Coulson looked at Fitz and nodded so Fitz turned on the sound and opened the mics.

“Raina what’s going on?” Coulson spoke. Raina immediately stopped her waving and looked right at the cameras.

“Coulson, I had another vision. Strucker, Whitehall, they are going to use it on Skye. Loki’s scepter, they are going to use it to take over her mind. I don’t know when but sometime soon.” Raina was out of breath, the words tumbling out of her almost faster than anyone could understand. As the words sunk in everyone went cold. Clint’s eyes found Coulson’s.

“We can’t let them do that to her. We have to get there before that happens.” Clint said.

“We have to risk it, Tony do what you have to, get the Iron Legion ready. Everyone grab your gear and head to the Bus. We are wheels up in no more than a half an hour.” Phil commanded.

Everyone nodded and hurried out of the room leaving Coulson behind, looking at the screen.

“Raina, thank you… is there anyway you can tell me how this is going to go? Are we going to save her?” He questioned.

“I’m sorry Coulson. I haven’t seen it. I only just started to nod off when I saw them using the scepter on Skye, I didn’t see anything beyond that. I can’t tell if you will be able to change it or not. I have no idea how these visions work. I’m sorry I can’t be more help.” Raina said sadly, sinking back onto the bed in the corner of the room.

“No, Raina you have done so much. Thank you. I promise, once Skye is home safe, we will help you understand your powers too. Just get some rest.” Coulson said before turning off the feed and hurrying out of his office to get his own gear. He was ready, they were going to get her back, no matter what.

Line Break

It had started out as a pretty normal day for Wanda and Pietro, or at least what passes for normal when you are prisoners of Hydra. They had been brought food, taken turns sitting on the bed whilst the other sat on the floor. Swapped stories of home. Then things had changed.

A guard came by around midday and beckoned them both forward. They followed without question, both of them were long past questioning orders. They followed the guard to the gym where he stopped and opened the door for them both to enter. They did and he shut the door behind them.

Inside the room they saw Dr. List, Dr. Whitehall, and Strucker all standing around a punching bag which was being attacked ferociously by Skye. Wanda’s eyes widened when she saw her but she immediately tried to quell any outward reaction to Skye’s state. She chanced a glance at Pietro and even though he too was trying to show no reaction to Skye’s appearance, she could see the horror in his eyes.

Skye had dark, angry bruises running up both of her arms which were clearly visible in her sports bar. Her long sleeve shirt was in a slightly bloody pile a few feet away from her. Wanda’s eyes sought out the source of the blood and she saw that both of Skye’s hands were bleeding and there was also a small pool of blood on the gauze on her stomach.

Wanda couldn’t understand what she was looking at. Until now Skye had been refusing to do anything for Hydra, the thoughts that Wanda had seen had been clear, Skye would rather die than do anything Hydra orders her to do. So why was she now attacking that bag as though her life depended on it, letting three heads of Hydra stand around and watch her like she was a toy. The men had such smug, self-satisfied smiles on their faces that Wanda knew would make Skye’s blood boil. Why was Skye ignoring them now?

“Ah, so glad you could join us.” Strucker noticed the twins enter the room and beckoned them both over to join the three men watching Skye. Wanda and Pietro took slow, careful steps over. They were wary of what their purpose was here and what Strucker had in store for them. Out of the corner of her eye Wanda eyed a case on a table, she wondered at its contents.

“Wanda, would you be so good as to share with all of us what is going on in Skye’s mind?” Dr. Whitehall asked. Wanda hadn’t had many interactions with the man yet since he had only just arrived when Skye did but she didn’t like him. She knew what he was capable of, what he had done to Skye. She had warned Pietro to stay away from the man if he could. Wanda turned to Strucker who gave her a nod before she complied with Whitehall’s order.

Wanda turned her attention back to Skye. From where she was standing she could only see the side of Skye’s face. She had never entered the girl’s mind while she was conscious, Skye was always asleep or unconscious when Strucker had her enter her mind in the past. Wanda wanted nothing more than to apologize to the girl, at the very least to look into her eyes and try to convey how sorry she was for what she was about to do. It was no use though, Skye never looked away from the punching bag, she never stopped hitting, kicking, her assault on the bag was frenzied and endless. With no choice but to obey, Wanda entered Skye’s mind.

Instead of the useless depressing amount of self-hatred and self-doubt, the memories of good times with her team, the feeling of emptiness that seemed to consume her recently, Wanda found no emotions. In fact, there were barely any thoughts at all, just one thought, one phrase, repeated over and over:

“Train. Train. Train. Train….”

It was an endless loop. There was no emotion attached to it, no emotion at all. It was like everything that made Skye Skye had been scraped out and replaced with a singular objective, train. With horror, Wanda retreated from Skye’s mind and looked at the smiling faces of the men around her. She turned to Strucker.

“She can only think one thing ‘Train’. She has no other thoughts. No feelings.” Wanda said, she wanted to demand that they explain what they had done to her but she knew she would be disciplined if she spoke out of turn.

“Excellent, it is as we had hoped doctors. Ze staff has removed all of ze girl’s original thoughts and desires and replaced zem with whatever we tell her.” Strucker sounded giddy. It made Wanda sick.

“Indeed, you told her to train, thus the only thought in her mind is to train. She can conjure no other ideas.” Dr. List continued. Wanda felt Pietro slide his hand into hers and squeeze. She knew he was thinking the same thing as her, if they have a way to control Skye, eventually they will use it on Wanda and Pietro too.

“We have to test her powers, see if the staff has given her control.” Dr. Whitehall said. He turned to Skye and spoke.

“Skye, stop.” She didn’t, she kept up her assault on the bag. Whitehall turned a puzzled expression on Strucker.

“That’s enough Skye.” Strucker said. Skye immediately stopped, Wanda is pretty sure that if she could she would collapse to the ground. Instead, Skye stood up tall and turned toward the gathered crowd. Wanda had to suppress a gasp when she saw the unnatural blue of Skye’s eyes.

“It seems that since Von Strucker is the one who used the scepter on her, he is the only one she will obey.” Dr. List supplied.

“Perhaps… Skye you will obey everything I say as well as every order given to you by Dr. Whitehall, Dr. List, and every superior Hydra officer.” Strucker ordered. Skye did nothing, no outward acknowledgement that she had even heard him speak. Strucker turned to Wanda.

“What is she thinking now?” He questioned, Wanda entered her mind. Just like before there was a single thought on repeat.

“Obey Strucker, obey Whitehall, obey List, obey Hydra.” Wanda said. Strucker smiled and nodded at Whitehall.

“Skye, take two steps forward.” Whitehall instructed. Skye did as he ordered immediately, no hesitation.

“Kneel.” List ordered, Skye did. Wanda thought she might be sick.

“Brilliant, she obeys without question. This scepter is truly remarkable.” Whitehall said.

“Enough of zis, stand girl.” Strucker said, much to Wanda’s relief. Skye stood.

“Use your powers to destroy zat bag.” Strucker ordered, pointing at the punching bag in the corner of the room. In an instant Skye spun around, threw out her arm, and blew the punching bag across the room. She advanced on the bag where it had landed with both arms outstretched. Wanda could see pulses of energy coming out of both of her hands, pummeling the bag. The bag burst and all of the sand within exploded across the room but Skye didn’t stop, she kept shooting her powers at the remnants of the bag.

“Skye, stop!” Whitehall ordered. Skye did, Wanda watched her sag where she stood. Skye was panting hard, her eyelids fluttered for a second as though she might lose consciousness but she didn’t. Instead, she once again stood tall and turned to face the men.

“We will have to be careful how we word things, it appears she takes our orders incredibly literally. We said destroy the bag, I don’t think she would have stopped until every last particle was destroyed.” List said.

“Agreed, I can’t wait to see how effective she is in battle.” Strucker said with a wicked smile.

Strucker had just finished speaking when a series of explosions rocked the base. Wanda lost her footing but was caught by her brother, she turned to see Skye pulling herself back to her feet from where she had fallen. The doors to the room burst open and an agent ran into the room.

“Sir, it is S.H.I.E.L.D. and the Avengers!” The agent yelled, at Strucker.

“Well, it seems we will get to see her in a fight sooner than we thought.” Whitehall said.

“Skye, stop S.H.I.E.L.D. and the Avengers. Kill them all.” Strucker ordered and Skye left the room.

Line Break

Everyone had gathered in the Bus in less than ten minutes and May had taken off as soon as they were assembled. It would be a longer flight than anyone was happy about but May assured Coulson that they were going at top speed when she joined everyone in the command center after putting the plane on auto pilot.

“Alright, we have several options for entry, but considering this is not a stealth entry the shortest path is the best. To that end I recommend the front door as our main point of ingress.” Coulson spoke to the agents and Avengers before him.

“Once inside we can split into teams, Tony, Fitz, Tripp together, Steve, Bobbi, Hunter together, May, Clint, and Mack together, and Nat, Simmons, and myself. Dr. Banner will stay on the Bus and prepare the med bay. Whoever finds Skye first will radio me, Nat, and Simmons and we will come to you. Simmons will render whatever aid is needed to get Skye transported to the Bus and relay whatever information is needed to Bruce. Once we get Skye out Bruce and Simmons will decide the best course of action. If she needs to go to a hospital we will determine the closest secure location to take her, if not we will come back to the base and treat her there.” Coulson explained while everyone nodded.

“As soon as the Iron Legion blows the ground defenses May will land us as close to the base as she can and we will go in. Speed is of the essence. We don’t know if they will try to kill Skye when they know we are coming. We have to get to her before that happens. We have to get to her before they can use the scepter on her.” Coulson concluded his briefing. A hush fell over the group.

This is it, everything they have been working toward for weeks. Saving Skye, bringing her home, they are hours away. Yet there is no feeling of relief washing over them, instead they are all consumed with anxiety, the fear of all of the things that could go wrong. They have no idea what they will face when they land, but none of them will stop fighting until Skye is safe.

“Tony, is the Iron Legion ready?” Coulson questioned.

“Yep, they are en route from the tower. They will beat us to the base by a half an hour. I have ordered them to wait at the coastline until I give them the order to attack. On your command, the missile defenses will be gone.” Tony replied.

“Great, we only get one shot at this people. Stay on comms, call for backup if you need it, and above all else take care of yourself and your partners. I don’t need to lose anyone else to these bastards.” Coulson said. He needed to make sure everyone kept their wits about them. He knew how easy it would be for them all to get tunnel vision and be so focused on saving Skye that they forgot to take precautions. He was probably going to have the same problem, but at least he could try to get in front of it now. Everyone nodded as his words sank in.

“Alright, gear up and be ready.” Coulson said and everyone turned to leave the room. Fitzsimmons and May lingering behind after everyone else had gone.

“We’ll get her back.” Coulson said to his assembled team, though he doesn’t know who he was trying to reassure more, them or himself.

“We will.” May said resolutely. Coulson turned and saw the conviction in her gaze and he felt himself growing more sure just by seeing the resolve she had.

“We have to.” Simmons said. Fitz reached out and grabbed her hand, giving it a squeeze.

“You two don’t have to come in. Tripp and Bobbi are more than capable of giving Skye first aid until we can get her out, you can stay on the Bus with Dr. Banner.” Coulson said, it was a discussion the four of them had had before the briefing. He was hoping they would change their minds now.

“No sir, we already decided. We have to come in. For Skye.” Fitz said, his tone and the firm glint in Simmons’ eyes leaving no room for debate.

“Alright, just be safe both of you.” Coulson said.

“We will, sir.” Simmons said with a small smile. May gave a firm once over to each of them before nodding.

“Go gear up.” They both left the room. May turned to look in Coulson’s eyes, holding his gaze for a long moment before nodding and leaving the room to take control of her plane.

Coulson squared his shoulders, letting the resolve of his team sink into his bones. They would save her. She would be coming home tonight. With these words in mind Coulson left the command center to join his extended team and gear up for the fight ahead of them.

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