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.
All Chapters Forward

The Call

Coulson hated this part of his newfound job. The part where he can’t focus on how worried he is for his pseudo-daughter. He would like nothing more than to wear his worry on his sleeve and put everything else aside to focus on getting her back from Hydra, preferably putting a few bullets in Grant Ward on the way to doing so.

But being the director means putting the big picture first. He will save Skye, that is not even a question, but he has to stop Hydra from doing whatever it is they plan to do with the Obelisk too. So, he prepares to split up his team and divert his resources away from saving Skye so that they can save the whole world instead. He tunes back into the world around him and listens as May lays out the gameplan.

“Director Coulson, Agent Triplett and myself will place the bombs. Fitz and Simmons will run things from up top.” May said.

Coulson trusted this team, he knew they could do this, but he also knows how high the stakes are here. He doesn’t know what that Obelisk can do but considering the lengths that Hydra has gone to, he is not taking any chances in case the worst does happen and they fail to stop Hydra from doing whatever it is they are planning. He waits until all the others have left the lounge area and turns to Agent Koenig.

“I want you and Billy to immediately return to H.Q. If things go radically South here, I want you to implement the Theta Protocol.”

Sam immediately reacts and tries to argue but Coulson cuts him off. He knows that calling in the Avengers is a pretty radical step, but considering they have no idea what the fallout will be if Hydra succeeds, he doesn’t have much of a choice.

Line Break

Skye’s head was spinning. Her father was supposed to be some monstrous serial killer, that was what she told herself. He had killed at least two people with a scalpel and his bare hands and then he had nearly killed Tripp, using his life as a bargaining chip to get away with his Hydra buddies. She came to meet him (at gunpoint, thanks Ward) and she was ready to face the monster from her past, instead she was confronted with a strange, confusing man who seemed to genuinely want to care for her.

How could someone who could do such horrible things also sit there and sing her a lullaby and get all choked up about missing her childhood. She didn’t know what to think, she just wanted Coulson and May to come get her. She just wanted to go home where things made sense. If she could talk to Coulson about all these thoughts and feelings maybe she could start to make sense of them all.

Instead, she was sitting here waiting to see if her crazy father was even going to survive whatever he had planned. He left her here so that he could go kill Whitehall, but Skye knew Cal would be no match for Whitehall and his goons. Her first time meeting her dad was probably going to be her last. That’s just typical.

She was interrupted from this increasingly dark and confusing spiral of thoughts by the Hydra asshole that had come to get her father barging in the door and grabbing her by the arm. She thought about trying to fight him off but she knew she wouldn’t get far. As soon as they made it out of the door two of the Hydra cronies with automatic weapons flanked her so she just decided to bide her time and go along with them for now.

As they kept walking she could hear the obnoxious voice of Daniel Whitehall talking to someone. As soon as she walked into the room all eyes turned to her. Ward started talking about how he only brought her to keep S.H.I.E.L.D. from shooting them out of the sky, but he wasn’t convincing anyone. Skye knew she was in a treacherous position, the way that Whitehall was looking at her had her instincts on high alert, not that there was anything she could do about it right now, they were completely surrounded by well-armed Hydra agents.

Then Whitehall’s creepy version of Agent May stepped up and opened a secure box that held the Obelisk inside and held it out towards Skye. She knew what was coming next.

“I’d like you to pick it up.” Whitehall said with that grin on his face that Skye wanted nothing more than to punch off. Instead, she said, “You first.” Whitehall’s only reaction was to widen his smirk while one of his cronies stepped up and cocked his gun pointed at Skye’s head.

With a grimace, Skye moved up and grabbed the Obelisk out of the box. Instead of the expected horrific pain, Skye felt an inexplicable pull, a draw to somewhere close by. She wanted to follow it for some reason, her own preservation instincts were fighting against her for a split second and saying to go where the Obelisk wanted. She ignored the feeling and lunged for the nearest guard, pressing the cursed thing to the exposed skin on his neck and he collapsed in agony. She saw her father attacking another guard out of the corner of her eye and when she straightened up Ward and Agent 33 were having a stand-off.

Whitehall’s grin had turned into a full-blown smile as he said, “I hope you’re as special as your mother.”

Line Break

When Bobbi called with Hydra’s location Coulson was flooded with relief. At least now they had a starting point. The problem then was what to do about the Alien City. After much debate and discussion, Coulson decided the risk was too great, no one was going to go down into the city until Hydra had been dealt with.

They needed all their specialists for the raid on the theatre and if they were able to stop Hydra from getting down into the tunnels in the first place, then there was no need to send anyone into the tunnels. Fitzsimmons would wait at the mouth of the tunnel in the citadel in case something changed, and they needed to go down there, but as long as everything went to plan, no one would be entering the city until after Hydra was long gone.

Now, Coulson, May, Tripp, Bobbi, and Hunter were in the quinjet parked on the roof of the theatre deciding how they were going to attack this situation. They decided to enter in teams, Hunter and Bobbi together, Tripp, May, and Coulson together. Once they entered and started their search, it didn’t take long for Coulson, May, and Tripp to decide to split up, all three desperate to find Skye.

Line Break

Skye was tied to a chair looking at her dad unconscious on the floor at her feet and trying not to think about the pull from the Obelisk. Her confusion was only getting worse. Apparently, Raina and her father weren’t lying when they said she was “special” I mean she could touch the alien buzzkill device when it killed pretty much everyone else who touched it. And considering Raina was the one who took it from her hands she was able to touch it too, just one more thing she was telling the truth about.

Once again Skye was pulled from her thoughts when her father startled awake in front of her, immediately asking if they had hurt her. Again, being all concerned for her. She didn’t know what to do with that concern, so she just shook her head no. Suddenly Whitehall walked in from the door over by Ward and started advancing on them.

“I’ve waited years for this.” Cal tried to attack Whitehall but instead Whitehall pulled out some kind of remote which he activated and Cal froze in place then fell to the floor. Skye saw some device on his neck and all the muscles around it were bulging out like they were all flexing. It looked painful. Whitehall crouched down in front of her.

“Do you know what your mother’s special gift was?” “No.” “She didn’t age. At least not like the rest of us. I wonder if that’s your special gift as well, or if your special in another way? Discovery requires experimentation.”

As he said this he tapped Skye’s knee and she wanted to punch him, kick, and scream at him to keep his hands off of her, but she couldn’t. So, she kept her calm like May taught her and showed no fear, no outward reaction. Whitehall looked down at her dad.

“I killed your wife, and before I kill you, I want you to watch what I’m going to do to your daughter.”

Before Skye could fully digest the horror implied by that statement there were gunshots and yelling in the distance drawing Whitehall and Agent 33 out of the room and leaving only one agent in the room to guard the three of them. She could see her dad fighting the muscle seizing thing, apparently Ward did too because he started distracting the guard.

As soon as Cal was freed from the device he came up behind the guard and snapped his neck. Ward immediately asked to be untied but since Cal is apparently crazy he decided that it was safer for both Skye and Ward to stay tied up. So, Skye was left tied up in a room with the person she hated most in the world, great.

Of course, it didn’t take long for Ward to get himself untied anyway. He came right over to unite Skye and treat her like a child along the way telling her, “Sit down while I check the door.” She wasn’t about to do that.

She was going to do what she has wanted to do for so long. Since he dropped Fitzsimmons in the ocean. Since he killed Agent Hand. Since he kissed her while she was handcuffed to a pole and tried to say that he loved her. Since he threatened to rape her when she wouldn’t love him back. Since she found Agent Eric Koenig’s dead body and knew that he was dead because of her. She grabbed the gun from the dead Hydra agent and shot Grant Ward 4 times in the chest.

“Never turn your back on the enemy. You taught me that,” and she left him there to die.

Line Break

Cal was stalking his way through the halls, he was going to finally get his revenge for Jiaying, for Daisy, for everything that had been stolen from them. He rounded the corner and stared at the back of Daniel Whitehall’s head. As he approached all he could see was Jiaying’s smile, all he could hear was his baby daughter’s laugh in his head. He was so blinded by his rage that he didn’t care about the gun Whitehall was pointing at him. Suddenly he felt a blinding pain in his shoulder then in his calf. Cal collapsed to the ground in pain.

He failed again, he didn’t kill Whitehall, instead Whitehall is looking down at him with that awful smile on his face. Was his smiling face the last thing that Jiaying saw before she died? Cal closed his eyes and waited for the pain of a final bullet, one that would reunite him with his beloved wife, but it never came. Instead, he felt a blow to his head and was thrown into unconsciousness.

Coulson rounded the corner and prepared to descend the stairs when suddenly he heard two gunshots coming from below. He began to creep down just in time to see Daniel Whitehall crack Cal across the head with his gun and knock him unconscious.

Two Hydra cronies ran up to Whitehall and he gave them orders to tie him up and bring him with them. Coulson was trying to decide how he wanted to handle these three when he felt the barrel of a gun pressed up against the back of his neck.

Agent 33’s voice said, “Drop it,” and all three men at the bottom of the stairs turned to look at them with both goons pointing their guns at Coulson too. He held his gun out in front of him and let it fall to the floor. She grabbed his hands and roughly slapped some zip ties on him then shoved him down the stairs toward Whitehall. Coulson stumbled down the last few stairs and fell to his knees next to Cal’s prone body at Whitehall’s feet. He looked defiantly up at Whitehall for a second then quickly turned to Cal and began putting pressure on his shoulder wound, he wasn’t going to let Skye’s father die.

Whitehall’s gleefully arrogant voice came from above him. “Director Coulson, so glad you’ll be joining us! I made a promise to Dr. Johnson here that I would make him watch as I experimented on his daughter, but you, you might be even more effective at getting her to comply. My sources say you and Agent Skye are quite close.”

“You touch her and I will kill you.” All Whitehall did was smile that fucking smile and tell his men to take them out and load them up in the cars.

Line Break

Raina heard all the gunshots and alarms start going off. She knew S.H.I.E.L.D. would come, she was just hoping that she would make it down into the tunnels before then. She watched as all the agents in the room who had been watching and operating the drill hurry out of the room to join the fight. This was her chance. She grabbed the Diviner out of the box and descended into the tunnels.

She walked along the tunnels with just a glowstick for light and was suddenly confronted by a massive man standing stalk still in front of her. He turned to face her and his eyes were completely black.

Raina said only one thing to him, “Take me there,” and the man turned and began to lead her straight to the temple. When he stopped walking Raina knew they had arrived and she walked past him to face her destiny.

She entered the temple and a light shone on a single raised platform in the middle of the circular room. She walked up to it and the Diviner began to glow in her hand. She let go and the Diviner floated to the platform. The doors around the room began to slide shut, sealing out the unworthy.

The anticipation and excitement in Raina had never been higher as she watched the Diviner open to reveal beautiful blue crystals within. As the Diviner finished moving suddenly dust exploded out of it. The dust cloud blew Raina back a few steps but nothing else happened for several long seconds.

Suddenly Raina began to feel something crawling on her hand. She raised it to the light and saw stone spreading across her hand, then looked down to see it spreading across her entire body. The excitement turned to fear as she began to feel like she was being suffocated by the rock. Maybe it was killing her. This isn’t what is supposed to happen. She is supposed to become beautiful, not be killed by some rock!

Before she could stop it, the rock had covered her whole body and plunged Raina into complete darkness. She felt nothing, then there was pain. So much pain exploding throughout her body, she tried to move, to scream, to do anything, but she was sealed into this rock. Then, as suddenly as it had started the pain subsided and was replaced with this sickening nausea that was unlike anything Raina had ever felt before.

She tried once again to move and this time she felt the rock begin to give way and crack off her body. Light flooded in and Raina fell to the ground as the rock fell away completely. She was so confused and scared that she went to put her face in her hands, but when she raised her hands she saw the hands of a monster.

Her very flesh had changed to something grotesque and thorny. This was not what her grandmother told her it would be, this was horrifying. Slowly the doors to the room began to open and Raina realized she could leave, but she didn’t want to, she wanted to stay here and undo what had just happened. She felt worse than she had ever felt before. Her insides felt like someone had shoved her full of gravel that was all rubbing together. As she moved her hands across her body she felt thorns everywhere. She wasn’t an angel. She was a monster.

She sat there for what felt like an eternity, just thinking, trying to find a way to fix this. Her eyes found the Diviner, still sitting there, opened like a flower. The brilliant blue crystals would be easy to reach, even easier to break. She realized that Hydra might still be interested to know what was inside the Obelisk. Maybe if she could show them, give them what they have been so desperate to get, they would help her reverse this. It was her best shot.

She reached out and broke off the biggest crystal she could and put it in her pocket. She picked up her glowstick and began working her way back out of the tunnels. As she ascended back into the theater, she resolved to find Whitehall and force him to fix her.

Line Break

May and Tripp regrouped and are slowly working their way through the lower levels of the compound. They come out of one door at the same time as Bobbi and Hunter are coming down the stairs to their right. Several Hydra agents entered the room from the opposite side and May, Hunter, Tripp, and Bobbi all made eye contact with each other and in perfect synchronization they shot all four of the Hydra agents dead.

May gave new orders, “Bobbi, Hunter, circle back and take care of any Hydra agents you find and try to keep anyone from following us, Tripp and I are going to find Coulson and Skye.” With that she and Tripp turned and left the room and Bobbi and Hunter went back the way they came to mop up any Hydra agents left behind.

Line Break

Skye was making slow progress through the compound but she didn’t really know where to go. She decided to just follow the gunfire.

She was climbing down some stairs when she saw a large pool of blood at the bottom. If it had been a Hydra agent who was injured or killed, they would have just left him where he was, but since there was no body, it was probably one of her people. The dread started to pool in her stomach and she turned to follow the blood trail, if it was a S.H.I.E.L.D. agent that was injured (not dead, Skye would not believe anyone had been killed) then they could have been taken by other S.H.I.E.L.D. agents to get medical help so following the blood trail would lead her to friends and safety. If they had been taken by Hydra, then Skye was going to get them back.

As Skye kept following the blood she started to hear more and more voices. She stopped with her back to a wall and peered around the next corner. She saw what looked like some kind of loading dock and a bunch of Hydra agents heading towards SUVs. Her eyes followed the trail of blood to the bleeding S.H.I.E.L.D. agent, but it wasn’t an agent. It was her unconscious father bleeding from his leg and shoulder. And Coulson was holding pressure to his wounds.

They were on the ground by the cars and as Skye watched two Hydra agents started to pick up Cal and move him towards an SUV while Coulson was hoisted to his feet by two others and shoved towards the same SUV.

Skye didn’t take any time to think, she threw herself out from behind the wall and pointed her gun at the men taking Cal and Coulson. She barked out an order at them all, “Just drop them both and you all can climb in your vehicles and leave!”

The Hydra agents immediately wheeled around to point their guns at her except the four agents with her fathers (not fathers, Cal and Coulson) Coulson looked horrified, “Skye no, they want you. You have to get out of here.”

Skye ignored him and pressed on. “They can shoot me but I will take both of you with me if they do.” She was looking only at the guys holding Coulson. She knew she was bluffing, she definitely wasn’t fast enough to take out two of them before being shot, maybe not even one of them, but they didn’t know that.

She could see the internal debate on the faces of the guys with Coulson, they didn’t have anyone here to give them orders so self-preservation was going to win out, at least that’s what she was betting on.

“We’ve been looking for you Agent Skye.” Skye flung herself around at the sound of Whitehall’s voice but it was too late. Agent 33 pounced on her and tackled her to the ground. She cuffed her hands behind her back and brought her up to her knees at Whitehall’s feet. He wore the same look as before, sizing her up as if she was some kind of mystery he couldn’t wait to solve.

Coulson was yelling at Whitehall, pleading with him to let Skye go, but it fell on deaf ears. Whitehall finished staring at Skye and he turned to nod at Agent 33 who smashed Skye on her head with the butt of her gun while another agent did the same to Coulson.

Right as the agents turned to resume loading the cars, Raina emerged from the building. All the agents stopped to stare at her. Whitehall spoke, “Who are you?”

“I went into the temple Dr. Whitehall. I learned what was in the Diviner, and what it does to people like me.” She pulled the crystal out of her pocket and held it up to the light. “I will give you what you have always wanted, I will give you what was inside, but you have to promise to fix me.”

Whitehall was stunned but absolutely intrigued by this new form, he was eager to get his hands on this crystal sure, but now he was even more eager to get his hands on Raina. He pulled a smile on his face and spoke.

“Raina, of course I will help you. Like I said, you have earned my trust. If you give me the crystal, we can go together to a new facility where we can learn exactly what has happened to you and how to fix it.”

Raina wanted to be relieved, but something felt off. She stepped toward Dr. Whitehall and held out the crystal, when out of the corner of her eye she saw agents coming up from behind her. She dropped the crystal and swung out her hand to swipe at them. Her newfound nails caught the first in the throat and he fell to the ground bleeding. The second she kneed in the groin and then she took off running, out of the loading dock and away from the theater.

Several shots rang out but they seemed to glance off her thorny shoulders. She glanced back as she rounded the corner and saw Dr. Whitehall smiling, holding the crystal.

Dr. Whitehall felt happier than he ever had. He had the daughter of his greatest scientific achievement and her husband and he had the director of S.H.I.E.L.D. Now he also has the secret to the Obelisk. Everything he has been working for since Peggy Carter tore him down during the war is finally about to come to fruition. He can’t wait to get started.

The Hydra agents loaded all three of their unconscious captives into cars and began to pull away just as Tripp and May poured out onto the dock. “No! They took them, they took Coulson and Skye!” May screamed at Tripp, he had never seen her lose her composure before, but as fast as it was lost she had regained it. “We need to regroup with the others and track those cars. We can’t lose them!”

Line Break

Fitzsimmons were sick of waiting with no idea of what was going on. They had been sitting here at the top of the citadel tunnel for hours now waiting to hear that Skye was okay or that they needed to go down into the tunnels themselves because things had gone bad.

Instead, they hadn’t heard anything from anyone and the worry was starting to get to them. Fitz’s phone was glued to his hand, just waiting for news. They both had their comms in even though they knew that the rest of the team wasn’t using them. They were staring into the tunnel hoping for some kind of sign that something had happened. It came in the form of a voice.

They began to hear a voice echoing up from the tunnel. They both looked at each other to make sure that the other person had heard it too, then they got up and leaned over to look down into the tunnel and try to hear who that was.

“Hey, I’m down here, I’m back!” Fitz’s eyes lit up as he looked at Simmons, “Mack!”

They sprang into action, sending down the rope and harness to bring him back up. As soon as he reached the top they began to pepper him with a million questions, talking over each other like they used to. Mack climbed out of the harness and yelled out a short, “Hey.” They both abruptly stopped talked talking.

“I’m ok, as far as I know, and back in control of myself, but we need to warn the others and get out of here. Raina set off the Diviner.”

With one quick look at each other Fitzsimmons once again sprang into action. Simmons and Mack started to grab all the gear they could and Fitz pulled out his phone.

“Koenig, have you heard from anyone?” “No, not since they went dark.” “Yeah same here, but Mack just came out of the tunnel. He seems to be cured of whatever was controlling him but he said that Raina was down in the tunnels and she set off the Diviner.” Fitz heard a sharp intake of breath followed by a long pause. Then Koenig spoke, “Are you guys evacuating?” “Yeah we are going to head back to the Bus and wait, hopefully whatever apocalyptic thing Raina just started doesn’t reach that far.” “Okay. I have to make another call.” Then Koenig hung up.

Fitzsimmons and Mack hurried out of the citadel and back to the Bus to wait and pray that the rest of their team would show up and that they didn’t just fail to save the world.

Sam Koenig looked at his brother, “Do you think this is what Coulson meant when he said ‘radically South’?” Before Billy could reply his own phone rang, he picked it up immediately, “Koenig” “Billy, its May. Hydra took Coulson and Skye.” Billy placed his hand over the receiver, looked at his brother, and said, “Make the call.”

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