Theta Protocol

After Whitehall’s nurse had taken blood from her and Coulson the real experiment had begun.

They had started with a lumber puncture. Dr. Whitehall had called in the two guards from before to unlock Skye’s left arm and leg then resecure them to the same side as her right arm and leg so she was lying on her side facing Coulson. They had pulled down the sheet exposing her naked body to the entire room. She felt humiliated and dehumanized by the entire thing. She had tried to close her eyes but Coulson wouldn’t let her.

“Skye, look at me. It’s gonna be ok. Just look at me.” She had locked eyes with him as he tried to give her a reassuring smile while she felt a cold fluid being applied to her lower back.

“Director Coulson, you shouldn’t make promises you can’t keep.” Whitehall’s voice had gloated from behind her. Coulson paid him no mind, he just kept his eyes locked on Skye. He saw them preparing a massive needle and bringing it closer to her. All he wanted to do was shut his eyes and pretend that this wasn’t happening but he wouldn’t do that to her. If he couldn’t save her from this torture he would make damn sure she knew she wasn’t alone in it. Cal hadn’t stopped struggling and howling into his gag next to Coulson but he didn’t acknowledge him. No one else mattered but Skye.

Coulson saw the fear in her eyes, she looked like she was shivering. She had no idea what was going on behind her but she knew it would be bad. They hadn’t done anything to numb her so they both knew this would hurt. Coulson nodded at her as Whitehall came down with the needle.

Skye’s eyes shut as soon as he pierced her skin, she took a few harsh breaths hoping that was the worst of it but then he began to press. She felt it moving forward and the pain grew until she felt a pop and she began to scream. It felt like it lasted forever but it was probably over in 5 minutes. Coulson was talking to her the whole time, trying to get her to breathe, but she couldn’t focus on him. Finally, the needle pulled out. Skye felt her whole body go slack. She stopped clenching her fists and she opened her eyes. Coulson was trying to smile at her but she saw tears brimming in his eyes. She offered him a quivering, wet smile in return, realizing she was crying too. She looked over and saw her father, he looked like a wild animal. His whole body was shaking as he struggled against the chains. When he realized she was looking at him he stilled.

“I’m ok.” Skye said to both of them. Cal’s struggles started up again upon hearing her speak but Coulson just nodded at her and tried to send that confidence back to her.

“You will be ok.” Coulson said, staring her deep in the eyes.

“Well, your mother handled that with much more grace.” Whitehall had moved to stand between Skye and Coulson. She heard a distinct growl from the direction of her father when Whitehall mentioned her mother.

“While she’s in position lets perform a bone marrow exam, both aspiration and biopsy.” Whitehall spoke to the nurses standing behind Skye who shuffled to gather materials. It seemed there would be no time for Skye to rest or get her bearings before they started on the next procedure. Coulson couldn’t take it.

“Hey, give her a break! She’s had enough!” Coulson screamed at Whitehall. Whitehall didn’t respond to him simply looked to the guards and gave them a nod. They moved in and roughly gagged Coulson just like they had done to Cal, punching him across the face and then giving him a couple kicks for good measure.

“Stop it! You said you wouldn’t hurt him!” Skye screamed.

“He was warned not to try to interfere Skye, there are consequences for not following directions.” With that, Whitehall turned back to his nurses. Skye looked down at Coulson who struggled to return to a sitting position after catching his breath. He nodded at her to say he was ok.

The nurses behind Skye applied antiseptic to her hip. One of the nurses then handed Dr. Whitehall a scalpel and he began to bring it down towards Skye’s hip without hesitation. When she saw the scalpel Skye renewed her struggles.

“No, no please!” She begged him to stop even if she knew it was useless. Whitehall pointed the scalpel in his hand at Coulson.

“If you continue to squirm Agent Skye, I will turn this scalpel on your beloved director.” Whitehall threatened. Skye immediately stilled, she looked at the scalpel and then to Coulson. Skye couldn’t be the reason they hurt Coulson. She would cooperate.

“Besides, you don’t want to move while I’m cutting.” Dr. Whitehall said with an evil gleam in his eyes and a smile on his face as he turned back to Skye’s body. He brought the scalpel down to her hip and made a small incision. Skye grit her teeth and tried to remain still. Then one of the nurses handed Whitehall a needle. Whitehall inserted the needle into the incision and applied pressure until he had punctured Skye’s bone. She screamed as he broke through. When he pulled out she gasped in relief until the nurse handed him another needle and he repeated the process. She creamed even louder the second time.

“Bandage the site. Once they are done you two return her to her initial position.” Whitehall ordered first the nurses and then the guards. The nurses were not gentle as they bandaged her. One of them held pressure on Skye’s hip, causing her to grunt in pain, and then the other placed a large gauze bandage over the wound. Once they were done the guards approached and unlocked her left arm and leg then turned her onto her back to lock her up as she had been before. To her great relief, once she was secured, one of the nurses covered her body with the sheet once again.

Skye tried to take deep breaths as her back and hip were jolted with pain every time she was moved. The guards were not gentle tugging her onto her back and restraining her and every little movement felt like agony. She turned her head to the side, eyes searching out Coulson. He gave her a weak smile, the best he could manage around the cloth shoved in his mouth. Skye noticed he had blood dribbling from his nose where the guards had punched him.

Whitehall started talking again, “I can’t find anything in her blood results. Start the analysis on the new samples while we begin the lymph node biopsy.”

“Yes, sir.” One of the nurses said and they moved out of Skye’s view, taking the syringes full of the things they had taken from her.

Whitehall approached Skye and smiled at her again relishing the look in her terrified eyes, “Still no discovery from you my dear. That means more experimentation.” Silent tears began to slip down Skye’s cheeks and she closed her eyes. The next thing she is aware of is more antiseptic being applied to her neck. Her eyes fly open and she immediately tries to jerk her head away from the source. Whitehall calls to the guards outside to restrain her head. One of the guards comes over and roughly grabs Skye’s head, holding it at an angle so the nurse is able to resume preparing Skye’s neck.

“I’m not doing anything to cause you permanent damage Skye. Once your special gift has revealed itself to me you will be of much more use alive than dead. You don’t need to look so scared.” Whitehall’s words sounded like they were supposed to be comforting but they only sent further fear racing through Skye’s spine.

“We’re ready doctor.” The nurse said.

“Right, let’s proceed.” Whitehall said as he clapped his hands together.

Whitehall walked around so he was once again behind Skye. The nurse handed him a scalpel and he brought it down to Skye’s neck.

“Don’t move Skye, one false move and I can’t promise the damage won’t be permanent.” Whitehall threatened, before cutting into the side of Skye’s neck. She screamed as he cut the tender flesh of her neck. She heard mumbled voices but it was like she was underwater. She couldn’t hear anything right, she didn’t dare to open her eyes, keeping them squeezed tight shut. Her teeth were clamped shut as she screamed past them. She felt more tools digging around in her neck and she felt like she might pass out from the pain but as much as she wanted to she couldn’t. She felt as if something was tugging at her insides and then the instruments in her neck were removed.

Skye went slack against her bonds, against the hands of the guard who was holding her head still. She drew in a ragged breath as the pain began to lessen. She vaguely heard Whitehall order someone to “Stitch her up.” Then Whitehall was in front of her.

“Oh no Agent Skye. You will remain awake for this.” He said with a sigh as he reached into his pocket and pulled out a packet of smelling salts. He pressed it to Skye’s nose and her eyes jolted open and she began to cough. Every cough sent an agonizing wave of pain through her neck. She felt tears flowing down her face and something wet running down her neck. Her brain helpfully supplied the knowledge that it was probably blood.

“You tried to go to sleep Agent Skye. That won’t be happening anytime soon.” Before Skye had a chance to comprehend his words more pain shot through her neck and she flinched instinctively against the hands holding her head which only made them tighten painfully. The nurse had begun stitching up her neck without warning.

“Can’t have you bleeding out or catching an infection can we. Not when we still have so much to look forward to.” Dr. Whitehall said with his sinister smirk firmly in place. He watched her grit her teeth and hiss in pain as the needle and thread repeatedly tugged at her neck for a few more moments before he straightened up.

“I will be in the lab analyzing the new samples. One you have finished cleaning her up leave them all alone for a while. You, remove their gags.” Whitehall declared as he left the room. The guard not holding Skye’s head moved forward and took the gag out of first Coulson’s mouth, then Cal’s. Once the nurse had finished stitching and bandaging Skye’s neck he told the guard to release her head and then they all left the room. They closed the door behind them with a resolute bang.

For a while it was quiet, no one spoke. At some point during Skye’s torture Cal had fallen silent. Coulson glanced over at him now and saw the man collapsed against the wall. His eyes held a faraway look to them. Coulson decided he was in a state of shock. Skye had closed her eyes while the nurse was stitching her up and she still hadn’t opened them. Coulson was growing worried the longer she went without opening them.

“Skye, hey Skye. Open your eyes sweetie. Come on, look at me.” She took a second to respond but slowly he saw her eyelids flutter open. Her eyes searched around the room before finally landing on him.

“Coulson.” She whispered his name. He smiled at her.

“That’s right, I’m right here.” He waited until she seemed more aware of her surroundings before pressing on.

“How bad is it?” He asked.

“It hurts. It hurts so much, all over.” She started crying again, she couldn’t stop the emotion from overtaking her.

“I know baby girl. You are so strong. You are one of the strongest people I know. I know you can survive this. The team is coming. May is coming. She will save you. You’ve gotta focus on that, you’ve got to believe that.” He pleaded with her. He needed to know she wasn’t giving up. He needed to hear her say she was still in this fight.

“I know, May will never give up on us.” Relief flooded through Coulson as she said those words.

“That’s right Skye, she will never stop fighting. Neither of us will stop fighting for you.” Skye gave Coulson the best smile she could muster before closing her eyes again. He let her rest.

Line Break *Start Here*

As soon as the quinjet touched down Jemma was on her feet, collecting her tablet and Raina’s blood samples. The moment the ramp was low enough she started walking to Coulson’s office, where she imagined the rest of the team and the Avengers would be gathered. She could hear Bruce following her and she knew Tripp would be right behind them. She had given the techs instructions to unload the equipment and samples collected, as well as the obelisk, and take everything to her lab so she could study it when she was done briefing the team.

Jemma opened the door to Coulson’s office and was met with a very crowded room. Normally it would have been comical to see so many high ranking S.H.I.E.L.D. agents and Avengers crammed together like this but she didn’t take the time to enjoy the thought, she just marched behind Coulson’s desk where May was.

“May, we found out what Raina did in the temple.” Jemma wasted no time getting to the point.

“Tell us Simmons.” May stepped aside, sensing that Jemma needed access to the desk. Jemma immediately started hooking up her laptop to the system while she continued talking.

“Dr. Banner, Agent Triplett, and myself went into the alien city with several techs to collect samples and determine what had occurred while the rest of the tech team went to the theatre to sweep through what Hydra had left behind there. When we entered the temple we found the obelisk, it was open.” As she said this she pulled up a picture on the screen at the back of the room causing everyone to turn and look. Several eyebrows rose and jaws dropped as they all took in the sight of the obelisk folded back with blue crystals growing out of the center of it.

Jemma continued, “We did not attempt to take samples of the crystals while in the field out of fear that we didn’t have enough time before Hydra may return to collect some themselves. Dr. Banner and I opted to slice the obelisk off of the platform and place it in a containment case to return the whole thing to the base. It is being offloaded into my lab as we speak. Once it is in an isolated container I will sample the crystals and try to determine what they are and what they might do.”

“Ok, anything else?” May asked.

“We determined that the walls of the city were all carved out of lava rock, leading us to believe that none of them were load bearing. We decided the best course of action in order to stop Hydra from possibly trying any of this again was to blow several of the walls on the ocean side of the city and flood it. We used Agent Triplett’s Howling Commando tech to set off several timed detonations and the city is now comfortably under water.” Jemma said.

Steve’s ears perked up when he heard Dr. Simmons mentioned the Howling Commandos but he figured it was not the time to ask so he decided to ask Agent Triplett about it later.

“Also, the team at the theatre found some… concerning security footage from the loading dock. It is of the moment Agent Skye and Director Coulson were captured.” Simmons continued.

“Show us.” May demanded. Simmons pressed another button on her tablet and now the security footage was playing in the back of the room. With all eyes turned away from her, May allowed herself to show just how angry she was when Agent 33 made Skye kneel in front of Whitehall and then knocked her unconscious. She had clenched her fists so hard that Simmons was afraid her nails had to be cutting into her palms. She reached out and gently touched May’s arm, the older woman relaxing slightly under the touch.

"Who is that and why does she have agent May's face?" Steve asked. Simmons paused the video.

"That's Agent 33, she was an Agent of S.H.I.E.L.D. but she was captured by Hydra and brainwashed. She doesn't have a choice in what she does for them. She has my face because she was wearing a nano mask posing as me when I electrocuted her in the face." May said.

"Damn." Tony said. Simmons shook her head and resumed the video.

The room watched as the Hydra agents resumed loading the cars when a figure appeared from the building. “What?” Clint whispered while across the room Hunter muttered “Bloody hell.” They were all stunned by the strange, thorned person talking to Dr. Whitehall, holding one of the blue crystals that they had just seen coming out of the obelisk. They watched as the figure attacked several of the Hydra agents that tried to catch it and then fled, taking several shots to the back as it went. The feed cut off as they all watched Dr. Whitehall holding the strange crystal while Cal, Coulson, and Skye were loaded into the cars. They all turned back to look at Simmons.

“The team collected several blood samples from the ground from where she had been shot. I have not been able to examine them, but when I do, I think I will find that that figure was Raina.” Simmons said.

“Why do you think that?” May urged her to continue.

“Based on the timestamp, this person came out of the building just before Mack was informing Fitz and I that Raina had entered the temple and activated the obelisk. He didn’t see her come out but that figure had one of the crystals from the obelisk in its hand. There was a crystal in the obelisk that looked as though it had been broken. No one saw her after she emerged from the temple but she is the only one who could have taken the crystal. I will test the blood samples to confirm it but I believe that whatever she did to activate the obelisk somehow changed her into that.”

The room was quiet for a moment with everyone thinking about this new revelation.

“It makes sense. According to what she told Skye she was able to hold the obelisk without being killed by it, Mack you said she was carrying it into the temple right?” Bobbi questioned.

“Yeah, and clearly whatever that city was doing to control me wasn’t happening to her.” Mack said with a grimace.

“So there was definitely something special about Raina, maybe this was it.” Tripp said with a nod, having entered the room just after Simmons began her debrief.

“Thank you, Simmons. When we are done here if you would please confirm that it was in fact Raina that would be appreciated. Fitz, she wasn’t captured by Hydra so there is a chance she is still in the city, if you could try to track her through security footage-” May said.

“I’m on it.” Fitz cut her off.

“Good, in the meantime we have been trying to find a way to track down Coulson and Skye. So far Fitz hasn’t found anything in Hydra’s records and we haven’t been able to track any suspicious planes leaving San Juan at that time.” May continued.

“What about Bakshi?” Bobbi asked from the side of the room.

May quirked an eyebrow at her suggestion while Clint said, “Who’s Bakshi?”

“He was Whitehall’s right-hand man. Ward caught him and left him gift wrapped for us as a sort of present for Skye a while back. When he started to accidentally give things away during my interrogation, he broke a cyanide capsule in his cheekbone and tried to kill himself but unlucky for him we managed to save him. We have him locked up downstairs. If anyone would know where Whitehall took them it would be Bakshi.” Bobbi said looking at May.

May nodded and said, “I agree that he would know but he has already demonstrated that he won’t give things up voluntarily. The only things we got out of him were things that we pieced together from syntax, he never actually broke. I don’t want to waste days breaking him while Coulson and Skye could be going through hell right now.”

“Well then we won’t interrogate him.” Clint said with a smile, looking at Natasha. She smiled back at him and picked up where he left off, “We let him think he’s been rescued and get him to lead us right to Whitehall.”

“Go on.” Steve said, a bit confused.

“We tell him he’s being transferred and then while he is being driven the car he is in gets ‘attacked’ by Hydra and he is rescued. Only it will be one of us and he will tell that person where he wants to be taken in order to meet up with Whitehall. Once that person has the location they tell the rest of us and we converge.” Clint says.

“We’ve done it before, works like a charm everytime.” Natasha adds on.

“It should work May.” Bobbi says.

May nods, “Alright. We need someone good undercover who he hasn’t seen before and who he won’t recognize from the news. Hunter you up for it?”

“Absolutely ma’am.” Hunter says with a fake American accent that has most of the room rolling their eyes.

“Great, the rest of us can dress in Hydra gear, complete with face mask so he won’t recognize us as we attack the car. I will be in the transfer truck, Bobbi you ok to join me?” May asks.

“Yes ma’am.” Bobbi nods.

“Natasha, Clint, Steve would you be ok joining the attack team. We could use the numbers to make it seem believable.” May says.

“Of course.” Clint says while Natasha and Steve nod.

“Great, Clint, Natasha, Hunter, Steve, and Bobbi will stay here with me to iron out the rest of the plan. Everyone else get back to work.” There are nods of agreement around the room as most people shuffle out.

Line Break

Bobbi walked down the stairs to the cell, she let down the electronic barrier. “Up and at ‘em Mr. Bakshi. You are being transferred.” She smiled at him as he stiffly sat up on the bed, staring daggers at her the whole time.

She cuffed him and marched him up the stairs and to the hanger where May was waiting with the car. They loaded him in the back and took off. They had decided to plant some ideas in his head on the drive so Bobbi started talking.

“I don’t like this May, transferring him when we still don’t know where Whitehall took Skye.” They weren’t going to tell him that Coulson was also missing but they wanted him to know that Whitehall had taken an agent since that may effect where Whitehall would be hiding.

“I know Bobbi but we need Talbot’s help to find Skye so handing over Bakshi to the government is worth it. Besides, Bakshi’s not that important of a pawn anyway.” They wanted to undervalue him as much as possible to really trigger his borderline personality disorder, it would make him that much more desperate to find Whitehall.

“I guess you’re right. With Talbot’s help, finding Whitehall should be easy enough anyway.” Just as the words left Bobbi’s mouth the car was hit on the driver’s side. The attack went down just as planned. May and Bobbi ‘killed’ all the Hydra agents and then they were blindsided by one who took them by surprise and ‘killed’ them both. Bakshi bought into the whole thing, eagerly climbing into the SUV with Hunter and driving off. As soon as they were out of eyesight everyone got up off the floor. Nat jumped on the bike that was waiting in the truck that hit Bobbi and May and sped off after them, keeping everyone apprised of their location over comms.

“Great plan Clint, I especially like the part where everyone ends up covered in fake blood.” Bobbi said, ending with a punch to Clint’s arm.

“Hey, there’s always a price for strategic genius, at least this one you can wash off with a hot shower.” Clint said with a smirk.

“No time, everyone back to base. Clean up, suit up, and get to the bus. As soon as Bakshi takes Hunter to Whitehall we go in. Let’s get our guys back.” May said, jumping in the truck. She felt adrenaline pumping through her veins, finally they were going to get them back. Finally her family would be together again.