Theta Protocol

The flight back to base was a somber one. When May didn’t protest when Clint and Tripp offered to pilot, everyone that knew her knew she was in a bad place. Instead, she sat in the lab and watched as Simmons wrapped Coulson’s ribs. Fitz was with them. Everyone left them alone, realizing that they needed to be alone for a while.

“How was she sir? I mean I know she was hurt and in pain but… how was she?” Fitz asked after Simmons had finished wrapping Coulson’s ribs and they had all fallen silent.

“She was scared and hurt, really tired… she didn’t give up. She trusts you guys to save us. Just like I did.” Coulson said.

“Well, she shouldn’t. We didn’t save her.” May replied quietly.

“We will May. She knows that we will come for her no matter what happens. She believes in us.” Coulson says as he tries to get May to look at him.

They are all silent for a while after that, all of them knowing that they can’t make each other feel better. The only person who could make them feel better right now is Skye. Simmons is the one who eventually decides that they need to begin to move forward so she decides to fill Coulson in on what they found in Puerto Rico.

“Sir, Dr. Banner and I recovered what was left of the Obelisk from the temple in San Juan. It is definitely where that crystal came from and there are more of them that are still connected to it. We have isolated it in a sealed container back at base and begun to test samples. It is conclusively alien but we can’t determine much else about its properties.” Simmons says. Coulson, May, and Fitz respond to the information in the way that she was hoping. They all straighten up and seem to refocus on the task at hand.

“We also recovered the security footage of the loading dock from when you and Skye were taken. We have the footage of Raina coming out of the building. What Dr. Whitehall said about her was true, she came out of the temple a completely different person, covered in thorns.” Fitz continued where Simmons left off.

“The Hydra agents shot her as she fled but the bullets seemed to glance off her. I tested the blood samples she left behind and they are unlike anything I’ve ever seen before. She has extra macromolecules that should not be possible in a human. I am sorry to say that Dr. Whitehall must be right that those crystals are what changed Raina which is why they changed Skye too. I have agents looking through all of our files to try to find any mention of a person with this same occurrence in their blood.” Simmons finished.

Coulson took a deep breath and nodded his head as he absorbed the new information.

“Alright, when we get back I want you guys to keep at it. Running any tests you see fit, hacking, searching, scouring, whatever you can. Take whatever resources you need to find Skye. If you need help from Stark or Banner just ask, I’m hoping they will stick around for the search. Then again maybe they will just leave, I’m sure they are all furious with me.” Coulson concluded sadly.

“Actually Phil, they have all come to the same conclusion, Fury is the one they should be angry with, not you. That’s not to say they aren’t still pissed, but I think they are gonna stay to find Skye.” May told him much to his surprise.

“Ok, good. Well, I will talk to them once we are back at the base and make sure the hatchet is buried and see what they plan to do. In the meantime, I’m gonna get a change of clothes from my bunk.” Coulson said as he carefully stood from the table to leave the room. He gave Fitzsimmons each a nod before he left the room. May followed him out.

As he ascended the stairs he felt May’s presence at his back so Coulson stopped on the landing above the cargo hold and turned to face her. She stepped up to him and they just looked at each other for a long moment, gathering strength from each other. Slowly, Coulson reached out and took one of May’s hands in his and gave it a squeeze, then just as slowly he let go. May stepped back.

“I’m gonna go check in with Clint and Tripp, see how much is left in the flight, and retake control of my plane.” May said. Coulson just gave her a small smile as she turned to leave. He shook his head to clear his thoughts then straightened his shoulders as he entered the common area of the plane. He walked past the kitchen and couches and saw Bobbi, Hunter, Mack, Stark, Banner, and Steve. They all looked up at him as he passed but he didn’t really acknowledge any of them, not wanting to be drawn into a conversation with them at the moment. As he opened the door to his office he was unsurprised to find it already occupied.

“You guys waited longer than I thought.” Coulson said with a huff as he closed the door behind him and walked around to stand behind his desk and face Clint and Natasha properly.

“We thought about accosting you as soon as we found you, but it didn’t seem appropriate.” Clint joked halfheartedly.

“Thanks for your self control.” Coulson replied.

“We get that Fury ordered you to keep your resurrection a secret, and he will get his own visit from us at some point, but how could you not tell us Phil. If it had been one of us and Fury gave that order there is no way in hell we would have followed it. Not when it comes to the four of us.” Natasha replies, because she, Clint, May, and Coulson have always been closer than simply being a team, they were a family. They had a trust that Natasha doesn’t give out easily and the fact that Coulson didn’t tell her has made her question if she can ever trust him again.

“I’m so sorry. Really, I am, but you have to believe me when I say that it wasn’t about you. After I was stabbed I wasn’t just gone for a few seconds and then brought back. I was dead, for days. There was a program from years ago that apparently I was in charge of called T.A.H.I.T.I. where scientists were using the recovered body of an alien to extract blood, spinal fluid, anything they could get to make all kinds of serums that they were using to treat agents with terminal illnesses. When the agents began to suffer terrible, life destroying side effects we had to erase their memories to cure them. When I saw the terrible toll of these experiments I recommended to Fury that the project be shut down and it was. Except when it came to me. He decided that he wasn’t willing to let me die. He used alien blood to bring me back. According to Dr. Streiten when I was brought back I had lost the will to live. They erased my memories of what had been done to me, my memories of the program, and made me believe that I had only been dead for seconds and then I had been sent to recover in Tahiti. I was gone, recovering from what they did to me, for months.

“When I finally came back I didn’t know what had happened, I just wanted to get back to work. May and I started the team and threw ourselves into working outside the command structure. Meanwhile I started to have flashes of what had been done to me. When I was kidnapped and I finally remembered what happened Fury gave me the file and told me what had been done. It wasn’t long after that that Hydra came out of the shadows and we were fighting our own people. Then Fury put me in charge of rebuilding S.H.I.E.L.D. and I had no time to think about anything else. I knew you guys were ok, I have been in contact with Maria a few times and she assured me you were safe. That was the best I could do. I promised myself that once I had time I would reach out. Obviously, that didn’t happen. I should have made the time. You have no idea how sorry I am that you had to find out about me being alive because I was in danger again.” Coulson finished with a sigh. He didn’t expect all of the words that had just come tumbling out of him. It was probably a symptom of all the guilt he felt but once he started talking he couldn’t stop.

“Next time I see him, I’m gonna kill Fury.” Clint said after a moment of silence.

“Agreed.” Natasha said. They both sank down to sit in the chairs in front of Coulson’s desk and Coulson felt a smile cross his face. They were letting their guard down, maybe he had a chance to salvage his relationship with them after all. Coulson sat down too.

“I felt the same way, until he saved Fitzsimmons from drowning in the ocean and helped me take down Garrett. Though I did yell at him. A lot.” Coulson said.

“Fine maybe I won’t kill him… are you really ok now?” Clint asked.

“Yeah, it took some time. After figuring out what had been done I was messed up for a while, then when we used the alien blood to save Skye too I was too worried for her to focus on me. Then Garrett used the same stuff on himself to try to repair an old wound and he started to experience the same side effects that we had erased the other test subjects to stop. When I saw what he had been carving into the walls it triggered the same urges in me. It wasn’t until I saw the blueprint for the alien city in San Juan that the urges were cured. Somehow seeing the full picture stopped it. I haven’t had any problems since then.” Coulson said. Clint and Natasha both nodded as they absorbed the information.

“What about Skye? I mean you said you had to use the blood on her too, has she had any side effects?” Natasha questioned. She was surprised that May hadn’t told any of them that Skye also had the same alien blood in her that Coulson did.

“Yeah, on one of our missions before S.H.I.E.L.D. fell she was shot by Ian Quinn. He did it on Garrett’s orders, he thought that shooting one of my agents would force me to uncover how I had been resurrected in order to save her, and it worked. Skye was shot twice in the stomach at extremely close range. When I found her she was dead, she wasn’t breathing, she didn’t have a pulse. Luckily there was a hyperbaric oxygen chamber in the room and we put her in there to keep her alive and get her some medical help but all they could do was stabilize her and put her on life support. She wasn’t going to wake up. The only way to save her was to find where I had been treated and give her the same stuff. When we found the place that’s when I found out it was alien blood. It tried to stop the team from giving it to her but it was too late. It didn’t matter though, she has never had any side effects. Now that we know that she is like Raina, able to touch the obelisk and be changed by those crystals, I’m starting to wonder if that’s why.” Coulson concluded with a shake of the head.

“May said she has had a hard life, I guess she wasn’t exaggerating.” Natasha said. They were all silent for another long moment.

“So… are we ok?” Coulson asked.

“Yeah… just don’t ever think about keeping a secret like this from us again.” Clint said with a smirk.

“I want to punch you in the face, but I’m afraid I would aggravate your existing injuries so I will settle for the apology… this time.” Natasha said with a glare.

“Thanks… I really missed you guys.” Coulson said as a smile crept across his face.

“Missed you too man.” Clint said and he stood up to shake Coulson’s hand. Natasha stood beside him and gave Coulson a smile.

“Well, we should be landing soon, so we’ll leave you to clean up.” Natasha said and she and Clint left the room.

Coulson leaned on his desk with a deep sigh feeling like at least one weight had been lifted off his back. Now he just had to get his girl back.

Line Break

When Skye woke up she couldn’t understand what she was feeling. More specifically she couldn’t understand what she wasn’t feeling, she couldn’t feel her feet, her legs, her arms, or anything else below her neck. She whipped her head around and realized she was in a medical room of some kind and she was laying on a metal table. She still had her sweatpants on, thank god, but she didn’t have her top on, again. She should feel cold, but she didn’t. There were no restraints on her arms or legs this time, but she still couldn’t move no matter how hard she tried. Tears slowly started to run down her face as Skye realized what this meant.

“Oh, good you’re awake Skye. I didn’t want to start without you but my colleagues were getting anxious to begin.” As Whitehall entered the room several others entered behind him. They were all wearing surgical garb. She recognized one of the other men from before who had been standing with Dr. Whitehall outside her cell.

“If you have no objections Dr. Whitehall, I recommend we begin with the internal surgeries, the partial nephrectomy, cholecystectomy, and appendectomy.” Dr. List spoke from one side of Skye’s body.

“A fine idea Dr. List, I would also like to do a liver resection and remove several lymph nodes and one ovary.” Dr. Whitehall responded from the other side of Skye.

“I know you are confused Skye but all this technical jargon just means that we will be removing pieces of your kidney and liver, and taking your gallbladder, appendix, several lymph nodes and one of you ovaries. Don’t worry you will still be able to procreate. We might need that in the future.” Whitehall smiled down at her as he spoke.

She felt her head beginning to swim and her breathing shallow, she couldn’t even speak up to try to argue or refuse. She could barely breath, her vision tunneled, and she couldn’t hear the words being spoken anymore. She started to feel the bees buzzing in her head once again but no shaking seemed to escape her body. She tuned back into the world around her when she heard a voice near her head say, “Doctors, look!”

Skye looked down at herself and saw black and purple bruises forming all along her arms and up to her shoulders. She didn’t understand what was happening to her.

“Well, well, well, my dear. Are you trying to use your powers? It seems that my theory was correct, without the use of your body you can’t create vibrations outside of yourself. It looks like you are doing a marvelous job of shattering your arms though.” Whitehall smirked.

“Doctor, we cannot have her destroying herself during zis procedure if you recall.” Strucker spoke from outside of the room where he was watching through a window.

“Yes, yes, I know. Well, I’m afraid we will have to administer some drugs after all. Let’s give the patient some antipsychotics and mild sedatives, nothing to knock her fully unconscious but enough to make her relaxed and compliant please.” Whitehall spoke.

Skye saw a nurse approach her and then inject something into an IV that she hadn’t realized was connected to her. She slowly felt herself start to melt into the table. Her brain felt like mush as she tried to form coherent thoughts. Her eyes seemed to have trouble focusing on anything. She thinks she sees hands with scalpels coming down towards her body, but she can’t make sense of it since she doesn’t feel any pain connected to it. Her head lolls to the side and she sees all kinds of people holding different containers. Suddenly things start to be put into the containers. She looks to figure out where the things are coming from, and she realizes that they must be coming from her since her stomach is opened up on the table in front of her. She can’t understand how but she doesn’t feel concerned about it. She sees blood everywhere and hands are inside of her, but it doesn’t hurt so Skye decides not to worry about it. Suddenly piercing eyes are leaning over her, staring into her soul. Even with all the drugs flowing through her Skye knows she is afraid of these eyes. She turns her head away. A voice floats down to Skye through her haze, “Discovery requires experimentation.” Skye closes her eyes and feels a nonexistent shudder run through her. She prays for this to be over soon.

Line Break

Slowly, very slowly, Skye swims back to consciousness. She lets out a low groan as she tries to open her eyes and the lights blind her and give her a pounding headache. She squeezes her eyes shut and tries to take an inventory of her situation with them closed.

All she feels is pain. Her torso feels like it’s on fire, every breath she takes sends a jolt of fresh pain through her. She tries to breathe as shallow as she can but it does nothing to dull the pain. She raises her arm to hold her stomach but then pain rushes through her arm too. It feels heavy and weird. She tries to mover her other arm but she is met with the same feeling. She slowly opens her eyes again, squinting against the bright light, and looks down at herself.

Her arms are encased in splints from her fingers up to her shoulders, she has an IV in the hand that is closest to the edge of the bed. She looks to her body and is only somewhat relieved to find that she is wearing a shirt again, but the shirt is pushed up enough to expose the massive gauze and bandages wrapped around her stomach. Skye closes her eyes again and tries to take slow, deep breaths.

Slowly the memories of what happened filter through to her. She breathes slowly and fights off the panic as she realizes all that they did to her. She remembers the image of their hands inside of her and knows that it will haunt her for the rest of her life. She feels the tears leaking from her eyes and makes no effort to stop them.

“Good morning, Agent Skye.” Skye’s eyes snap open and she peers at the man standing at the window to her cell. It’s the man from before with the monocle. She vaguely remembers Whitehall calling him Dr. Strucker.

“I apologize zat Dr. Whitehall can’t be here to welcome you back to reality but he and Dr. List have so much work to do now zat zey have extracted all zose samples from you. You really are a goldmine my dear.” He says with a smile that makes Skye feel like she is about to lose the very small amount of food she has in her stomach.

“We are supplying you with a light sedative to keep you compliant while you heal, but once you are well enough, our fun can begin. You will be an invaluable weapon for Hydra’s future. I can’t wait to get started.” Dr. Strucker said before turning on his heel and walking away.

Skye closed her eyes tightly and tried to relax. At least that meant that nothing was going to happen to her today. She had at least a little time to recover before whatever fresh hell they would unleash on her. She turned her head to look at the wall. The cinderblock wall was sorta like the walls in the playground. If she let herself, she could almost pretend that she was in her bunk back at the base. Maybe she was injured from some mission and Jemma was being strict and forcing her to stay on bed rest while she recovered. Pretty soon May was going to come in and bring her tea and an ice pack with the wordless acknowledgement that she cared about her and wanted her to get better. Then Coulson would come in with his famous grilled cheese and sit with her for a while to make sure she ate and wasn’t too lonely. After that Fitz, Tripp, and Mack would bring in a tv with a gaming system hooked up and they would play call of duty or something that would take her mind off of being trapped in this bed for days on end. Eventually Bobbi and Hunter would show up with a bunch of different kinds of junk food. Every so often Jemma would come in to check on her and change her bandages.

Suddenly the door slammed open and Skye violently flinched causing pain to ripple through her entire body. A guard came in with a tray with some kind of soup on it and a water. He placed it on a table near the bed then left without a word.

Skye wasn’t home. She wasn’t going to eat Coulson’s amazing cooking or be comforted by May’s stoic presence. She wasn’t being mothered by Jemma or distracted by her friends. She was alone. With the enemy. They were going to hurt her more, torture her more.

The team is looking for her though, they are coming. Coulson isn’t here, maybe they saved him already. She won’t consider the idea that they might have killed him while she was unconscious. She has to hold out hope, Coulson told her that May would be coming to rescue them and she believes him, she believes in her family. They will save her.