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 Temple

Jemma took a deep breath as the lift lowered her down into the tunnels. Even with the hazmat suit on she still felt vulnerable to this place. They had no idea what had happened to Mack so they had no concrete evidence that these suits would keep it out. It was a risk she had to take if it could help them find Coulson and Skye. The sooner she was done here the sooner she could join the rest of the team in the search for her missing friends.

“You seem nervous.” Bruce’s calm voice spoke from Jemma’s right, cutting through her spiraling thoughts.

“I’m just concerned about all the unknowns we are dealing with.” Jemma responded as politely as possible. Normally she would be fangirling over the Avenger and world-renowned scientist that she was working with but with everything going on, she was having trouble not snapping at him for being so calm in such a dire situation.

“And concerned for your friends.” It wasn’t a question Jemma noted, she took another calming breath and nodded.

“I wish I could be at the base with the team, helping to search for them, not here in the mess that Hydra left behind.” Jemma said with a sigh.

“Well hopefully with the two of us we can get through this quickly and join the rest of them.” Bruce responded with a comforting smile.

Jemma nodded and smiled back. Maybe he was right. With Bruce’s help she could work even quicker and get to the team as soon as possible. The lift hit the bottom and she saw Tripp’s smiling face. He reached out and opened the door so the two could exit the lift with all of their equipment boxes. As soon as the lift was empty Tripp pressed the button to send it back to the mouth of the tunnel.

“Welcome to the party.” Tripp said with his trademark smile.

“How many techs do we have working with us?” Bruce asked.

“5 will be joining us down here while three more go through all of the tech Hydra left behind at the theatre to search for possible leads.” Simmons responded.

“So how do you want to do this?” Tripp asked. He knew his main purpose for being here was to keep everyone safe but he would help with the science as much as he could if it meant being done faster.

“Well I would like three techs documenting as much as possible. Photographing, sampling, anything that they can. The other two will go with Dr. Banner and myself to the temple and act as our assistants as we determine what could have happened in there.” Simmons said.

“Well, I’m coming with you guys. Until we know that the temple is safe I’m not leaving anyone alone in there.” Tripp told them both, though he was speaking directly to Jemma. He had already lost two members of his team to Hydra, he wasn’t about to lose another to whatever they had started down here in these tunnels.

“Sounds like a plan.” Bruce said as the lift once more touched down next to them. The three of them turned to see three techs getting off the lift, all three had old school, non-electronic, cameras and specimen collection kits.

“You three, follow the map and begin documenting whatever you can. Pictures and samples. Under no circumstances are you to split up do you understand?” Simmons ordered. The three nodded and began to shuffle away.

Once the other two techs had made it down into the tunnels the group began to head towards the temple. Tripp was in the lead with his gun drawn, Simmons and Banner were in the middle, and the two techs were behind them. As they got to the entrance of the tunnel Tripp stopped the group.

“I’m going to go in first and make sure the place is clear, wait for my signal before you come in.” Tripp said.

“Copy.” Simmons responded. Tripp moved forwarded and turned sharply into the tunnel. Jemma felt like she couldn’t breath the entire time he was out of sight. She felt Dr. Banner’s eyes on her but she didn’t look over at him. She couldn’t take her eyes off of the doorway Tripp had entered into. Finally they heard Tripp’s voice.

“It’s all clear, but you’ve gotta see this.” Tripp called out. Jemma let out the breath she had been holding and she and Bruce moved in together.

When they rounded the corner into the temple, Jemma’s jaw dropped. In the center of the room, on some sort of raised pedestal, was the obelisk, and it was open. The metallic sides were bent back and shooting out of the center were these strange blue crystals.

“What the hell is it?” One of the techs muttered.

“I don’t know. But we can’t leave it here. This is what Hydra went to all this trouble for, they might come back for it.” Jemma responded.

“The metal part is what turns people to stone right?” Bruce asked.

“That’s correct. I have no idea what the crystals do.” Jemma said.

“Perhaps we can cut the stone pedestal and take the top off of it, thereby not actually needing to touch any part of the obelisk in order to transport it.” Bruce supplied.

“That could work, if we have a containment box large enough. Did you guys bring the containment boxes I ordered?” Jemma asked the two techs who were standing near the door of the temple.

“Yes ma’am, we brough several different sizes, they are up in the citadel.” One of the techs responded.

“Good, you should both go, take the lift back up to the citadel. Find a containment case large enough for the obelisk and at least some of the stone pedestal and something to cut through the rock. Stick together, no splitting up.” Jemma ordered.

“Yes ma’am.” The techs answered and they both hurried away.

“So do we think this could have triggered something to happen? Like some doomsday that will destroy the city?” Tripp asked.

“It doesn’t seem like it, but we have no way of knowing for sure what it did until we can get it to a secure environment and run some tests.” Bruce responded. He knew it was too risky to try to take samples from some unknown object like this in an equally unknown environment, especially when, like Dr. Simmons had said, Hydra could come back at any time.

“Well at least that’s some good news. If the city is safe we can leave here with this and get back to base to run our tests from there. No need to keep this here and further endanger anyone.” Jemma said.

At that moment the three techs who had been documenting the rest of the tunnels entered the temple.

“Ma’am, we have documented what we could and taken numerous samples. All of the walls seem to be made of lava rock. The only strange thing that we noticed was the same alien writing that Director Coulson had been carving was carved into the floor in several places. We photographed every occurrence of it.” One tech said.

“Thank you, you three should head back up to the Citadel and wait for us there.” They nodded and left as a group.

“If all the walls are made of lava rock that means that none of them are load bearing.” Jemma said.

“What are you thinking?” Tripp asked.

“You want to blow it. Flood this place so Hydra can’t come back.” Bruce answered for Simmons.

“I think it’s the only way to ensure that Hydra cannot try this again.” Simmons said.

“I’m in.” Tripp said, and Bruce nodded at Simmons to confirm he was in too.

“Tripp, can you fashion some sort of non-electronic explosion?” Simmons asked.

“I have some of my grandad’s old mechanical detonators. Just give me a little C4 and tell me where to place the bombs. This place will be underwater in no time.” Tripp smiled. Just then the two techs walked in with a containment case and a saw.

“Alright, Tripp and I will go back to the citadel to get the bombs and decide where to place them, Dr. Banner are you alright to lead the extraction of the obelisk?” Jemma asked. She felt weird ordering around an Avenger but he didn’t seem to mind.

“It would be my pleasure.” Dr. Banner said with a smile and he turned to the two techs and they began to work on the obelisk.

Line Break

Tripp had just descended back down into the tunnels to place the bombs. Dr. Banner and his team had successfully extracted the obelisk from the temple and placed it in the containment case. He and the other techs from the tunnels were now loading it and all their equipment onto the quinjets. Jemma was waiting at the top of the tunnel for Tripp to get back and then they could leave and join the team to look for Coulson and Skye.

Simmons had called the techs at the theatre looking through Hydra’s tech to let them know to wrap up their search and meet the team here so they would be ready to leave when Tripp was done. As she stood at the top of the tunnel waiting for Tripp, the three techs that had been at the theatre came in.

“Did you get everything we need?” Jemma asked.

“Yes ma’am. We collected several computers along with files and equipment that might prove useful. So far nothing has pointed us to a location on the Director or Agent Skye.”

“Ok, well we will get more people on it back at the base. Load everything you have onto the quinjet. Good work.” Jemma said.

“Ma’am one more thing. We also got security footage from the loading dock.” One tech said.

“Fitz already looked at that, there was nothing on there to help us track Hydra.” Simmons said.

“Yes ma’am, but Agent Fitz likely only watched the video starting when the cars pulled out. We watched it from the beginning, before Hydra left, and we saw something strange. A person, or something, came out of the building just after Hydra had captured Director Coulson and Agent Skye. They spoke to Dr. Whitehall. We don’t have the audio, but the person clearly tried to offer Dr. Whitehall something. He tried to capture them instead and the person ran off but not before the Hydra agents shot them a few times. We collected blood samples of whatever it was from the ground.” The tech seemed scared just talking about this which only put Simmons more on edge.

“Show me.” Simmons said. The tech pulled out his tablet.

Simmons watched as Coulson was escorted out of the building by several armed Hydra thugs then she noticed Skye’s father being carried by two others. Cal was unceremoniously flung to the ground next to Coulson and Coulson was applying pressure to what appeared to be gunshot wounds in Cal’s shoulder and leg. Then Hydra lifted Cal and Coulson from the ground to put them into the cars.

She saw Skye come out of the building with her gun leveled at the two guys holding Coulson. Even knowing how this would end, Simmons wanted to yell at Skye to run, but she held her tongue and kept watching. She watched as Dr. Whitehall and Agent 33 came up behind Skye. 33 tackled Skye to the ground and made her kneel at Whitehall’s feet making Jemma feel sick to her stomach, then both Skye and Coulson were knocked unconscious and loaded into the cars.

Suddenly Jemma saw all the Hydra agents turn and raise their guns at a figure that had just emerged from the building. The figure had thorns all over their head and hands. Simmons eyes went wide as she tried to comprehend what she was looking at. The figure raised its hand and even with the terrible resolution on the cameras Simmons could tell it was holding one of the crystals from the obelisk. As it held the crystal out to Dr. Whitehall it was being unwittingly surrounded by the Hydra soldiers.

Suddenly the figure turned and lashed out at the men, swiping at one with its hand and kneeing the other one before it took off running. The Hydra agents opened fire and the figure stumbled but didn’t stop as it disappeared from frame. Dr. Whitehall had caught the crystal when the figure had dropped it and he seemed to be smiling as he turned and entered one of the vehicles. The rest of the agents filed into the cars and then they drove off. Simmons looked up at her techs who all share equally concerned faces.

“You said you collected blood samples from when it was shot?” Simmons tried to keep her voice calm, she didn’t need them to know how freaked out she was.

“Yes ma’am.” The tech answered.

“Thank you. Send that video to my tablet please, and put those samples on my quinjet, then load up the rest of what you found onto the other quinjet.” The techs all nodded at her then left the citadel.

Simmons had no idea how, but she suspected that was Raina. No one had seen her after she had entered the temple with the obelisk. She was able to carry the obelisk and enter the city without protection, clearly there was something special about her. Maybe whatever thing she was trying to do with the obelisk had done something to her instead. If Simmons was right those blood samples would prove it. Her thoughts were interrupted by Tripp coming up from the tunnel.

“Alright, in five minutes that place will be underwater.” He smiled at her.

“Good, let’s go home.” Jemma said.

Line Break

They had been in the air for an hour now. Tony had gone downstairs to the loading bay for a little privacy. He said he wanted to call Pepper and tell her Coulson was still alive. They all knew she would be just as relieved and concerned as they were that he was no longer dead but now missing.

Mack had disappeared down to the garage/lab. He seemed to need some space so everyone left him alone.

Steve was standing in the corner like a sentry, observing everyone. He couldn’t stop thinking about Hydra. After all these years of believing they were gone, sacrificing himself to take them down, they still managed to come back and destroy more lives. Steve was finding it hard not to blame himself. If he had just made sure they were destroyed in the 40s none of this would have happened.

Maria had claimed the coffee table and couches to set up her laptop and do some work of her own. No one knew what she was doing but it was probably important.

Clint and Bobbi were sitting at the dining table talking. Bobbi was catching Clint up on her undercover time at Hydra and other missions they had been on recently. He particularly seemed to like hearing about how they took on Marcus Scarlotti. Clint was thrilled to hear that May beat the crap out of him. Bobbi’s ex Hunter was standing in the kitchen nearby, not so subtly listening and glowering at the two of them.

Fitz was still in the command center trying to find Skye and Coulson through Hydra’s financial records and anything else he could think of to hack. He kept mumbling to himself, “What would Skye do.” Natasha didn’t really know what that meant but she decided to leave him alone.

May was in the cockpit alone. Bobbi and Clint had both offered to copilot with her but she had immediately declined. Natasha knew she wanted to be alone but she also knew that was not a good idea. Nat wanted to talk to her old friend and figure out what was going on with her. She snuck out of the common area of the plane and went to the cockpit door. Natasha thought about knocking but she knew if she knocked she would be denied entry so she decided to just go in.

May didn’t turn to see who had come in, there was only one person currently on the plane brave enough to come in here when she clearly wanted to be alone. Natasha sat down in the copilot’s seat. For awhile neither spoke, each waiting to see who would go first. Of course, they were both equally comfortable with the silence so Natasha realized that she wouldn’t get anywhere if she didn’t initiate the conversation.

“So, how long have you been back in the field?”

“About a year before S.H.I.E.L.D. fell Fury came to me. He told me what had been done to Coulson and that he couldn’t go back to his old position. He asked me to come up with parameters for a team that Coulson could run that would also be able to contain Coulson if the worst should happen and he should experience side effects from the treatment. Coulson didn’t know when Fury told him to assemble his team that it was based off my evaluation. We both knew Coulson would want to recruit me. Fury was banking on my need to protect Coulson outweighing my desire to stay out of the field and he was right. It only took three missions running back end for me to realize that I couldn’t protect them properly if I didn’t get back out there.” May said.

“Coulson always told us you would come back to the field, you just needed time. I told him to leave you alone. I guess He was right all along.” Natasha responded with a sigh.

May smirked and said, “Well it was for Coulson.” Natasha could only smile to herself. Clearly May was still denying her true feelings for him.

Then Nat said, “What about the girl?”

“We picked her up on our first mission. We were trying to find a powered guy who had rescued a woman from a burning building but Skye found him first. She was living out of a van, hacking for the Rising Tide. Completely hated the government, S.H.I.E.L.D., basically anything that kept secrets from the public. All because her whole life she has been searching for her parents to know where she came from and the only thing that she was ever able to find was a single document, redacted by us, from the day she was dropped off at the orphanage. You can see why she didn’t like us.”

Nat nodded. She was shocked by the amount of affection May had in her voice but she wasn’t going to interrupt her.

May continued, “Well she decided to join us when Coulson made the offer but at first she just wanted to get her answers from within. Coulson gained her trust pretty quickly and she told him about her search. When he found out about the agents that had been killed to protect her, the fact that S.H.I.E.L.D. was the reason that she was constantly moved around as a child, we thought she would be devastated, maybe even want to leave. Instead, she said that S.H.I.E.L.D. had been there for her entire life, keeping her safe. She never blamed S.H.I.E.L.D. for the way she was raised, instead she completely committed herself to becoming an agent.”

“She helped us track down Ian Quinn who was working for the Clairvoyant and when we found him she went in alone to keep him from escaping. Quinn shot her twice in the stomach on Garrett’s orders. She was basically dead when we found her. We found the place where Coulson had been treated and used the alien blood that had been used to heal him to heal her. When Hydra was revealed to be within S.H.I.E.L.D. she stayed completely committed and loyal to Coulson. I have been training her ever since S.H.I.E.L.D. fell and she has become an amazing agent. I know everyone is worried about getting Coulson back, but we have to get Skye back too Nat.”

“We will.” Nat said. “She’s important to you. I’ve never seen you talk about anyone like this.”

“I don’t know Nat. She’s had a rough life, she doesn’t deserve this too. Hydra has been after her since she was a baby. We don’t know what they want with her, but it can’t be good. There has to be a reason that she was thought to be an 0-8-4. And those side effects from the alien blood, she has not had any of them. There is something different about her and I’m worried that whatever it is, Hydra knows it and they want it out of her.”

Line Break

Skye couldn’t tear her eyes off of Whitehall for a moment as he just smiled at her. Then she started to struggle against her bonds. She could barely move at all they were so tight. “What do you want with me?”

“Soon enough Skye. But first, what do you know about your mother?” Whitehall never took his eyes off of Skye as he spoke.

“Don’t you dare speak about her mother!” Cal screamed from the side of the room, he was straining every muscle against his chains to no avail.

“Dr. Johnson, if you can’t restrain yourself I will have you gagged.” Whitehall spoke to Cal, but still he kept his eyes locked on Skye.

Skye was trying not to show fear, to lock it down and keep a neutral, controlled expression on her face but she was worried it wasn’t working. She responded, “I don’t know anything about my mom, except that you killed her.” She tried to put more venom into her words, but she knew they came out sounding fearful.

Whitehall’s smile never wavered, “I first met your mother in 1945 in Austria when I was serving the Red Skull. We came across her group digging in the ground, looking for the Obelisk. I was looking for it too. When we found it, I allowed everyone in the entire group to hold it. No one could survive it. No one but your mother. She was clever, she didn’t want to pick it up. Of course, just like you, she didn’t have a choice.”

“I wanted to understand what made her different, why she could survive it when no one else had, but before I could, Captain America killed our great leader and we had to run. I was captured by Agent Carter and incarcerated for 44 years. When Director Pierce freed me, I found your mother. While I had aged 44 years, she looked the same as she had in 1945. Amazing. Well… Discovery requires experimentation.”

Cal screamed in anger at those words but Whitehall ignored him and pressed on.

“I performed surgery to discover your mother’s secret. For a week, I worked on her. Eventually I was able to take everything I needed to steal her power for myself and turn back the clock. I can’t wait to discover your secret too.”

“If you lay one finger on her I will tear you apart with my bare hands you son of a bitch.” Cal was screaming at Whitehall, his bandages on his arm and leg were stained red from where he had ripped his stitches open from straining against the chain.

Whitehall turned to the door and nodded at the guards standing outside. Two guards entered, one punched Cal hard across the face and the other caught his head as it was tossed back. Then while his head was being held they shoved a cloth gag into his mouth to prevent him from speaking.

Skye tore her eyes away from her struggling father and looked back to Whitehall, “But I’m not special, there’s nothing inside me. No secret thing to uncover.”

“We’ll see.” Whitehall said, then he and the two guards left the room.

Skye was horrified she had no idea what he could think was inside her but it wasn’t there, she didn’t know what to do. She was staring at the ceiling in a daze.

Coulson’s voice snapped her out of her head, “Skye, just look at me. Breathe ok.” She turned to look at Coulson. He looked pale and worried. She imagined she didn’t look any better. She tried to do what he said and took a deep breath. Coulson kept talking.

“We are going to get through this, you are going to get through this. May and the team are looking for us right now and you know she will find us. We just have to hold out and stay strong til that happens right?” Coulson gave her a small reassuring smile and Skye nodded back at him. He was trying to hide his panic and stay strong for her.

Coulson knew this was bad, May and the team were definitely looking, but he had no idea if they would be able to find them, especially in time. He had to do something to get Whitehall’s attention off of Skye. Considering the way he reacted when Cal screamed at him Coulson decided he would try to talk to Whitehall when he came back and see if he could distract him off of Skye and onto himself. There was nothing else he could do.

The door opened and Whitehall came back in, this time he had a surgical gown over his clothes. Two nurses followed Whitehall into the room, both also wearing surgical gowns. Coulson knew he had to try to distract them now or else it would be too late.

“Hey, why not start the experimentation with me, huh? I’ve got alien blood running through me.” Whitehall stopped advancing on Skye and turned to look at Coulson. Coulson kept going, “When Loki killed me, Fury used alien blood to bring me back. It’s how I knew about the alien city. The blueprints showed up in my head.”

“So Garrett was right, Fury did do something crazy to get you back. You know I thought he was on a wild goose chase, searching for some way to bring back the dead. I guess he was smarter than I thought.” Whitehall turned to one of the nurses. “Please take a few vials of blood from Director Coulson here. I would be curious to see if we can find any trace of this alien blood in his system.” The nurse nodded and started to gather some materials, Whitehall turned and spoke to the other nurse, “In the meantime, you and I will get started with Skye.”

“No! No, experiment on me and leave her alone!” Coulson yelled at Whitehall.

“Director Coulson, you are only human. Being injected with an alien substance makes you more interesting but you are still human. She is something else entirely and the only way to find out what is to get to work, so stop interrupting me or you will be gagged just like her father.”

“Coulson, its ok. I’ll be ok.” Skye looked at Coulson, she knew having to watch and do nothing was killing him but she didn’t want him to get himself hurt trying to protect her. She realized that this was inevitable so there was no use in getting Coulson hurt too.

Whitehall smiled at her, “Ah very good, I knew having the director here would keep you in line. As long as you cooperate Skye, he will not be harmed. I cannot make the same promise about you.”

Skye gave Coulson a weak smile, then she turned to look at Whitehall. She would look him in the eye as he hurt her, she wasn’t going to give him her fear.

Whitehall turned to the nurse, “Let’s start with blood, then we’ll get to the biopsies.”

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