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 Plane Ride

Everyone froze for a second as Skye lost consciousness. No one spoke, no one did anything. They couldn’t believe they had her back. She is here, in her parents’ arms. Well, maybe not her parents but everyone knows that is who they are to Skye. The only sound was the murmured words of comfort coming from Coulson as he stroked Skye’s face. He and May couldn’t take their hands off of her. May had one hand holding tight to Skye’s right hand and the other was cupping her cheek while Coulson did the same on her other side. They were oblivious to the world around them.

As Simmons went to tend to Skye, Tripp ran to help Hunter with Bobbi. Fortunately, she was already coming around on her own. She pushed both of them away as she used the wall to get to her feet.

“I’m fine.” She gritted out through her teeth.

“Stop being so stubborn Bobs. Let me help you.” Hunter replied while sliding himself under her arm so she could lean against him. She let him, only slightly embarrassed for feeling weak in front of everyone.

Natasha and Steve took over the situation, they had to deal with the unknowns in the room.

“Thank you for helping her, now who the hell are you? How do we know we can trust you?” Steve spoke first. Wanda had others things on her mind however.

“Pietro, they were using the tunnels to escape.” She said to her brother who nodded and took off. All the conscious agents and Avengers in the room tensed as he sped away. They needed to know what these two powered people wanted, none of them liked how much they didn’t know. Before any of them could ask however, Pietro was back.

“They are gone, they made it to the other side of the tunnel and must’ve had planes ready. I could not find them.” Pietro said to Wanda who grimaced. Steve looked at Tony.

“Jarvis, has the Iron Legion detected any planes taking off from the base?” Tony asked.

“No, sir. Would you like me to expand their perimeter?” Jarvis questioned back.

“Do it, J.” Tony said, he hated to think that Hydra had escaped again when he was supposed to be the one to stop that from happening.

“The tunnel is 3km long due SW. There is a hangar at the end of it for emergency escapes.” Pietro supplied helpfully. Tony relayed the information to Jarvis and told him to send the Iron Legion that way to try and pick up the trail.

“Why are you helping us? Are you enemies of Hydra?” Natasha questioned.

“It is complicated. We volunteered for Strucker’s experiments but when they were successful in giving us powers, we were no longer free to leave. We have been prisoners here for years.” Wanda responded. Natasha did not like the sound of that. If they had volunteered then they had shared Hydra’s values, at least at some point. Natasha opened her mouth to ask another question when Simmons cut her off.

“We don’t have time for this. Skye needs medical attention now! We need to get her back to the Bus.” Simmons barked at everyone. Their heads all snapped to Skye, the tension forgotten for the moment.

“Simmons, what do you need us to do?” Coulson asked. He wanted to get Skye out of here more than anything, get her to safety.

“Someone needs to carry her while I apply pressure to her stomach, she has a large incision that is bleeding and I can’t stop it here.” Simmons responded. Steve immediately stepped forward.

“I can take her.” Steve said firmly. No one argued. As much as Coulson wanted to be the one to carry her he knew he wouldn’t be able to get her up the stairs and all the way back to the plane. Skye needed someone steady right now, so begrudgingly Coulson and May stepped back while Steve came over and ever so gently lifted Skye into his arms and cradled her to his chest.

It was slow going with Steve carrying Skye and Simmons walking backwards in front of him while holding both of her hands firmly to Skye’s stomach. Mack and Tony were leading the group with Steve and Simmons right behind them. Fitz was walking next to Simmons, ready to provide aid if she needed it, providing silent support to her in the long trek back to the Bus. Coulson and May were staying close behind Steve and Skye, not willing to be any further from her than necessary. After them, Bobbi was leaning heavily on Hunter with Tripp on her other side to help if she got weaker or seemed like she might fall. He was wisely keeping his hands to himself unless needed. He knew Bobbi would kill him if he tried to help her when she didn’t ask for it, only Hunter could get away with that. Behind them was an uncomfortable Wanda and Pietro. They wanted to go with this group, they needed to go with this group, but they didn’t have to like it. The man who killed their parents, who tried to kill them, was leading the party. They were clutching each other’s hands firmly to keep calm. Wanda was focusing on helping Skye, that seemed to keep her calm. Bringing up the rear were Clint and Natasha. Clint was walking backwards, keeping one eye on the path behind them in case someone was stupid enough to try to sneak up on them. Natasha was keeping both eyes trained on the two potential threats in front of her.

During the walk, Simmons was slowly cataloguing Skye’s visible injuries. She was firmly in Doctor Simmons mode, compartmentalizing everything. She couldn’t let herself focus on the fact that this was her best friend she was holding together, her sister in every way that matters. She took another deep breath and glanced at Fitz who gave her a tight smile. She tried to return it but the look on his face told her she failed. She turned back to Skye and decided she needed to relay as much information to Bruce as possible so he could be ready when they got to the Bus. She began quietly speaking to Bruce through the comms, a private channel between just the two of them. She didn’t want everyone to know how bad she suspected Skye’s injuries were until she had a chance to do something about it. Bruce listened intently and said he would be ready with everything they would need when they arrived. Jemma silently thanked the universe for sending Bruce to help her with this.

Line Break

The journey from the base to the Bus through the harsh Arctic winds had been difficult, Steve and Simmons had tried to move as fast as they could but every time they sped up too much Jemma lost her hold and Skye started to bleed. Most of the group ran ahead of them to the warmth of the Bus and Steve and Simmons came in last. As soon as everyone was in May hit the ramp close button and told Clint and Tripp to get the plane in the air. Normally everyone would be stunned that May was letting someone else fly her plane but given the circumstances no one was shocked that she didn’t want to leave Skye.

Steve gingerly laid Skye’s tiny body on the bed in the med bay and stepped back to allow Jemma and Bruce to access her. He turned around to leave the lab and was nearly run over by May and Coulson as they rushed to Skye’s side. They moved to take Skye’s hands but Jemma stopped them.

“I’m sorry but you have to let us help her first. We will let you know as soon as she is stable.” Jemma said apologetically, then she shot a look at Steve who nodded and stepped between Skye’s bed and May and Coulson.

“We have to let them do their jobs.” Steve said as he ushered the two out of the room, the lab doors closing behind him. As soon as the doors were closed, May and Coulson pressed themselves up against them. They wouldn’t tear their eyes away from Skye’s body, even as Jemma and Bruce removed Skye’s bandages and clothing to begin their exam. Everyone else turned away to give the doctors and patient privacy but May and Coulson couldn’t help themselves, their eyes locked on Skye’s face.

Hunter had carefully helped Bobbi into one of the jump seats where she had immediately leaned her head back against the wall and closed her eyes. He knew she needed to be checked for head injuries but right now the only doctors on board were working on Skye, so he resigned himself to keeping a close eye on her until someone was free.

About twenty minutes later, Tripp and Clint returned, informing everyone that autopilot is set and they are on their way back to the base.

“So, who are you?” Natasha asked, causing everyone to turn and look at Wanda and Pietro. Even May and Coulson finally broke their gazes from Skye to look at the newcomers, curious to know why they had helped them save Skye. Now that they are in a secure location and Skye is being taken care of, Natasha is going to get some answers. Wanda and Pietro shared a look before turning to face the group. Pietro looking straight at Tony.

“My name is Wanda Maximoff, this is my brother Pietro. We are from Sokovia. Two years ago we volunteered for Strucker’s experiments. He was using the scepter to try to give people powers. I don’t know how many people he tried it on, but we were the only two survivors.” Wanda said. She knew they couldn’t lie. Their only chance of not ending up dead or locked up at the end of this was to tell the truth.

“Why would you do that, volunteer for that psychopath’s experiments?” Tony asked.

“Because of you.” Pietro sneered, taking a step toward Tony. Wanda held up her hand to stop him as Nat’s hand went toward her gun.

“What? What do you mean because of me?” Tony asked bewildered. He was certain he had never met these two before.

“Pietro.” Wanda said warningly. Pietro turned to her.

“No, tell us. What are you talking about?” Clint asked. Pietro doesn’t take his eyes off Wanda as he begins to speak.

“We were ten years old. Having dinner. Us and our parents. When the first shell hits two floors below, it makes a hole in the floor. Its big. Our parents go in. And the whole building starts coming apart. I grab her, roll under the bed and the second shell hits. But, it doesn’t go off. It just sits there in the rubble. Three feet from our faces. And on the side of the shell, is painted one word.” Pietro and Wanda lock their eyes on Tony.

“Stark.” With that one word from Wanda, Tony loses all composure. The color drains from his face. His legs begin to shake. He wants to tear his eyes away but he can’t stop staring at them. The others in the room look to Tony, unsure of what to do.

“We were trapped for two days.” Pietro says.

“Every effort to save us. Every shift in the bricks I think, this will set it off. We wait for two days, for you to kill us.” Wanda finishes. Her eyes taking on an eerie red glow as she speaks. Tony falls to his knees, Steve catching him and Coulson helping him to sit on one of the jump seats along the wall. Clint, Nat, Tripp, May, and Mack are now openly laying their hands on their sidearms, ready to defend Tony if either of the newcomers try anything. Tony starts stammering while Steve and Coulson try to calm him down.

“It’s not your fault Tony. You didn’t know. It’s not your fault.” Phil says.

“Not his fault! It was his weapons! He killed our parents, he tried to murder us!” Pietro shouts at Coulson causing the others to draw their weapons and point them at him.

“No, he didn’t!” Steve shouts back.

“Tony only ever made weapons for the U.S. government, what he didn’t know was that his partner at the time, a man named Obadiah Stane, was going behind his back and selling Stark weaponry to anyone who could afford it. He sold to terrorist groups, dictatorships, the kinds of people who would target civilians. Tony never sold a weapon to anyone who would destroy an inhabited civilian structure!” Coulson responded.

The room fell silent, no one moved. The S.H.I.E.L.D. side of the room was waiting to see what the newcomers would do. Wanda and Pietro were trying to comprehend what they were hearing. They had spent most of their lives hating Tony Stark. They had sacrificed their lives to Hydra in order to take Stark down. Now they are being told that they did all that for nothing. Wanda peered into Tony’s head and saw only regret, not that he had sold weapons to the wrong person, but that he hadn’t known, hadn’t stopped Stane sooner. She looked at Pietro with tears in her eyes.

“They are telling the truth.” She whispered to her brother. Pietro turned broken, sad eyes onto Tony.

“It… It wasn’t you?” Pietro asked.

“No, but it’s my fault. I should have known what Stane was doing all along. I was too wrapped up in myself back then to pay attention to what was going on in the world around me. If I had, maybe I could have stopped him.” Tony spoke quietly, the weight of guilt that he feels from his actions back then is something he battles with constantly but having two people right in front of him, two people who are paying for his mistakes, makes it worse than ever before.

“Even if you had known Tony, it may have still happened.” Steve said to Tony before standing up to speak to the twins.

“I’m sorry about what you have been through, but it isn’t Tony’s fault. Even if he had stopped Stane from selling Stark weaponry under the table, it’s possible that whoever bombed your building would have still done it, they would have just used another bomb to do it.” Steve said to the two devastated people in front of him.

Pietro had grabbed Wanda’s hand and was staring at the floor with silent tears running down his face. Wanda also had tears in her eyes but she refused to let them fall. She turned to the group.

“We are so sorry. We didn’t know. We have just been so angry for so long. We needed someone to blame. Forgive us Mr. Stark.” Wanda said to everyone’s surprise.

“I’m the one who should be begging your forgiveness. Whether or not it is my fault it was my name on that shell. My irresponsibility is what did this to you. I can never make it up to you. I’m just so sorry.” Tony said through tears. Wanda smiled weakly at him. The room fell into an awkward silence again, one that was much less tense than before as they all put away their weapons feeling that the two no longer posed a threat. Tony was trying to pull himself together while the twins folded into each other, seeking comfort from one another.

Eventually, that silence was broken by the lab doors opening. Jemma and Bruce came out, pulling off doctor’s masks and gloves as they exited. May and Coulson pushed to the front of the crowd of people to be right in front of the two doctors while everyone else pressed in behind them. Wanda and Pietro slunk to the back to give everyone else some space.

“How is she?” Coulson asked at the same time as May said, “Is she ok?”

Simmons opens her mouth to speak but no words come out. Doctor Simmons is refusing to take over and compartmentalize for her. Right now, she is just Jemma. Jemma can’t take anymore of this. She can’t detail all of her sister’s injuries to the rest of their family. She has already spent the last two hours treating them. She tries once more to speak but tears just roll down her face instead. Thankfully Bruce takes over.

“She’s stable. She is malnourished, she has lost approximately 7-10% of her body weight which is incredibly dangerous for such a short amount of time. Her arms are completely covered in bruises from her fingertips to her collarbones which is the result of numerous capillary ruptures and hairline fractures in her bones, best guess is that it has come from her powers. We have placed temporary splints on both arms until we can get better ones made. She has several broken and bruised ribs which we have bandaged to the best of our ability. She has a zygomatic fracture on her left cheek under a rather nasty bruise. Scans also revealed a grade 3 concussion. The most worrying though is her internal injuries.

Skye has undergone surgery in the past 3-4 weeks. She has had her appendix, gallbladder, one of her ovaries, and several of her lymph nodes removed. They also took pieces of her liver and kidneys. The incision runs the length of her torso. She appears to have been bleeding internally which is why Dr. Simmons couldn’t stop the bleeding in the field. Best guess is that when she used her powers she somehow destroyed the connection points where the tissue was beginning to heal. She basically shook the incisions apart, both internal and external. If it weren’t for the staff compelling her to, there is no way she would have been standing let alone fighting. We have sutured everything that we could, removing scar tissue to allow for proper healing, and closed her incision. She will need time, a lot of time. My recommendation would be that we don’t take her to the base. She needs more medical attention than you can provide there.” Bruce concluded, not looking at Coulson or May. He didn’t know if he could handle the devastation on either of their faces.

“Where should we take her then? We can’t take her to a hospital, it’s not safe for her. We need somewhere more secure than that.” Tripp spoke up when neither Coulson or May did.

“The tower. It’s safe, there is plenty of room for all of us, and I can get the best doctors in the world there to tend to her.” Tony said, having risen from his seat when Bruce began speaking. He wanted to feel like he could do some good to make up for all the bad and this was exactly what he needed right now.

Tripp looked at Coulson for some instruction. He couldn’t make this decision for them. Finally, Coulson tore his eyes away from Skye.

“Thank you, Tony. Bruce, can we sit with her?” Coulson didn’t care if they went to the tower or the base or anywhere else, all he cared about was that his girl had been through so much and right now she was in there alone.

“Of course.” Bruce said and he and Jemma stepped aside as May and Phil rushed through the lab doors, each of them heading to one side of Skye’s bed and grabbing one of her hands.

“Well, I will go change our course to the tower.” Clint said and he headed up the stairs. Bruce noticed Bobbi and Hunter at the back of the group and headed over to check on her. After shining a light in her eyes and running her through some concussion protocol he determined that she has a grade 2 concussion and he went to get her an ice pack from the lab. He slips in and out of the room without Coulson or May looking away from Skye. After getting the ice pack to Bobbi, Bruce recommends that she go up to one of the bunks where she could lay down and Tripp and Hunter help her up the stairs, with Mack right behind them.

After helping Bobbi and Hunter to Jemma’s old bunk, Tripp and Hunter took up a silent vigil in the common area. Neither of them spoke, not knowing what to say. They just wanted to be near their team in case they were needed. They couldn’t do anymore for Skye, but they wouldn’t let the rest of their team down.

Inside Jemma’s bunk, Hunter helped Bobbi to lay down with the ice pack nestled under her head. He was expecting her to go right to sleep, but instead she just stared at the ceiling.

“She looked so broken.” Bobbi spoke so quietly Hunter barely understood her.

“I know love. But she’s safe now. We are going to get her home and get her better.” He said, stroking Bobbi’s hair. She gave the tiniest nod as tears spilled down her face. She turned to look into his eyes.

“Will you stay with me?” She whispered.

“I’m not going anywhere.” Hunter responded, pulling up a chair and sitting down. He pulled Bobbi’s hand into his lap so he could hold it as he stroked her hair. She smiled slightly as her eyes slipped closed.

Line Break

After Bobbi, Tripp, and Hunter disappeared upstairs, Bruce goes over to Tony and offers to take him upstairs somewhere private. He and Jemma had heard the commotion outside so they turned on their comms and listened to what was said. He knows his friend needs somewhere to fall apart right now. Tony nods and lets Bruce lead him upstairs where Bruce shoves Tony into one of the empty bunks and closes the door behind them, wrapping Tony in a hug and refusing to let go until Tony breaks down into sobs in his arms. The two stay there until Tony has gotten through it and composed himself.

Line Break

After Bruce concluded his report on Skye’s condition, Jemma fled up the stairs. She needed to get somewhere quiet and contained so she could fall apart. She didn’t hear the footsteps behind her until she was trying to throw the door to the storage closet closed behind her and someone was catching it. She looked up into Fitz’s eyes as he stepped into the room and shut the door behind him. She fell into him, sobbing like she had when Skye had been shot. Some vague, unhelpful part of her mind told her that this is the same room she tried to escape to that time too which just makes her cry harder. Just like then, Fitz is here to hold her together. She clings to him, letting out all the emotion that she has been holding in since rounding that corner and seeing Skye screaming, flailing against Steve’s body. Fitz holds her back just as tightly. She feels his tears fall on her head and knows that he is crying too. They stay there until a voice tells them they are an hour out from the tower, long after they have both stopped crying, just holding each other.

Line Break

Nat and Steve are left standing in the cargo bay, staring in as Coulson and May hold Skye’s hands. They both wish they could do something to help the little family inside but they can’t right now, so instead they turn to the two newcomers at the back of the cargo bay.

“Why don’t you both come upstairs, its more comfortable than sitting down here and its going to be awhile before we reach our destination.” Steve offers, watching the hesitation pass over the other two’s faces. Pietro and Wanda look at each other for a long time, seeming to have a conversation without words before Wanda eventually turns to him.

“Thank you, we would appreciate that.” She says as they both stand from the jump seats they had claimed. They follow Steve up the spiral staircase as Natasha steps in behind them. Once upstairs Steve leads them to the small breakfast table and gestures to them to take a seat. They can see from where they are sitting that the two black agents are sitting on the other couches in the center of the plane and Wanda assumes that the Captain lead them over here so as not to disturb the two men. Natasha and Steve sit on a couple of stools at the counter.

Steve very kindly tries not to watch the pair, he busies himself with other things, occasionally standing up and stretching or pulling out his phone from his pocket to check on their progress toward the tower. Natasha has no such concern, staring at the two for the entirety of the flight. Wanda and Pietro alternate staring at each other or the tabletop, trying not to be bothered by the red headed Avenger staring so intently at them.

Line Break

Once the cargo bay is finally empty and they no longer feel eyes watching them, May and Coulson reach across Skye’s body and take each other’s hands. They each need the comfort that the other provides at the moment.

“She’s safe.” Coulson says quietly.

“But she’s not ok.” May says, choking on a sob that threatens to escape her.

“No, but she will be May. With time, we will get her there. We will be there for her, we will help her, and she will be ok.” Coulson says, looking into May’s eyes. She holds his gaze for a moment longer before turning back to look at Skye.

She looks so small. She has lost so much weight and what little is left is covered in either bruises or bandages or has wires and tubes poking out of it. May suppresses another sob as she tries to hold onto her composure. She just needs to see her wake up. She needs to see Skye’s eyes. Needs to hear Skye’s voice. Until Skye is awake it’s like this isn’t real. Like she isn’t actually here.

May knows that isn’t logical, that Skye is right in front of her, but May needs to know where Skye is in her mind before she can start to help her and until Skye wakes up she has no way of knowing. May forces herself to take a deep breath and squeezes tightly to Coulson’s hand as time passes. Eventually Clint’s voice filters through the plane telling them they are an hour out. She forces herself to let go of Coulson’s hand and forcefully pulls her torn and tattered mask back into place, ready to face whatever happens next.

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