Theta Protocol

“So where we off to Sir?” Hunter questioned Bakshi in his annoying American accent.

“Just drive, I will tell you when we get there.” Bakshi replied. So that means Hunter is just going to be driving up to a Hydra site with no way of letting the team know before he gets there. At least they could hear everything that was being said in the car through the hidden mics and he knew Romanoff was right behind him. All he had to do was drive, he could do that.

Back at the base, May had already washed off the dry blood and put on her mission suit, now she was in the command center on the bus waiting for everyone else to join her so they could take off. The plan was that they would trail Hunter and Natasha from the sky so that whenever Bakshi told them they had arrived at Whitehall’s location they could land and go in right away. While she waited Simmons and Dr. Banner came in.

“May, I’ve analyzed the blood we found on the ground. It appears to be Raina’s blood but something very strange has happened to it. There are extra macromolecules, things that should not be possible in human DNA. Whatever has happened to make her appear the way she does now, it has changed her on a cellular level.” Simmons said in a rush.

“And I have taken samples from the crystals in the obelisk. They are definitely alien. There are some components that I am able to identify but others that have no earthly qualities. There is not much that I can say for certain other than the fact that it is not from this earth.” Dr. Banner added on.

“Alright, thank you both. Are you going to be coming with us?” May asked the two.

“Yes, we have discussed it and agreed that Skye and Coulson may each need a doctor when we find them so having both of us on board will be beneficial. If that’s alright with you.” Simmons said.

“Of course, Simmons, but you don’t leave the bus unless we ask for you got it?” May was not going to let another one of her kids go out in the field and get themselves hurt.

“Yes May.” Simmons said with a nod.

“Dr. Banner, I’m sure that you and your team have protocols for when you go into the field so I trust you will do what you need to do.” May addressed him, she wasn’t going to tell him not to come in if he wanted to, she just wanted to know what his intentions were so she could be prepared.

“Typically I only come in after the battle is over to lend medical help if needed. That is unless there is a code green and the other guy is called for in battle. As long as that doesn’t happen I am happy to wait with Dr. Simmons on the plane until we are called for.” Bruce replied.

“Great, well why don’t you both grab whatever medical supplies you see fit and get yourselves set up in the garage as best as you can. It’ll have to serve as a lab for now. I had Mack move his vehicles out for the time being.” May ordered and the two doctors left the room. May lowered her head and put her hand on her forehead. She was not used to being the one giving the orders, just another reason to look forward to having Coulson back. No, she shook her head, she wouldn’t go down that path right now. She couldn’t get caught up in the worry or how much she missed them right now, she had to focus on getting them back.

“You good?” Clint asked from the doorway.

“Yeah, just need to get them back.” May said, straightening her shoulders.

“We will, we’re close May. As soon as Bakshi leads Hunter to the location we’ll go in. They will be safe in a few hours. Then me and Nat can beat the crap out of Coulson for keeping his resurrection a secret and everything can go back to how it should be.” Clint said with a smile on his face. He was glad he succeeded in getting a small smile out of May too.

“You know it wasn’t his choice to keep it from you. He wanted to tell you but Fury wouldn’t let him. He became so focused on figuring out how he was brought back that everything else got pushed aside. Then S.H.I.EL.D. fell and he had to be director. Personal stuff like finding you guys and making things right, they had to be put on hold.” May said to Clint, hoping he wouldn’t be so pissed at Coulson if he understood why he didn’t tell him sooner that he was still alive.

“Maybe Fury is the one who deserves the ass kicking huh.” Clint said.

May could only smirk back at him, Steve, Tony, Bobbi, Mack and Tripp entering the room before she could respond.

“Fitz-Simmons and Banner are down in the garage getting stuff situated. We are ready to go.” Tripp said to May.

“Alright, let’s go get our people.” May said and then turned to head to the cockpit with Clint following her to copilot.

Line Break

Skye was in some form of unconsciousness, Coulson couldn’t tell if she was asleep or passed out but he took comfort in the fact that she was resting. He took stock of the room as she slept. He noticed the cameras in the corners of the room, it made him shudder to think that Skye’s torment had been recorded by that sadistic bastard. There were more surgical tools on the counter behind Skye. Coulson was praying Whitehall didn’t use them.

To his right Cal seemed to be stirring out of his stupor. He hadn’t moved or said anything since Skye started screaming while Whitehall was cutting into her. Now he was sitting up and adjusting his arms to relieve the pressure from the chains.

“My Daisy. I failed her, I let him hurt her too. Just like he hurt her mother.” Cal’s voice was a hoarse croak from all the screaming he had done.

“You did everything you could to save her Cal, we both did. I’m so sorry this is happening to you again.” Coulson said, he was trying to comfort the man. This was the most lucid he had ever seemed and Coulson thought maybe they could finally understand each other. Sadly, watching someone you loved being tortured had a way of bringing people together.

Cal looked away from Skye’s unconscious form for the first time in hours to look Coulson in the eyes. “I know you love her too. I’m sorry I couldn’t understand before. I thought you were another person trying to take my baby away from me, but you were another person who could protect her. It’s my fault she’s being put through this.” Cal said.

“You can’t think like that Cal.” Coulson replied.

“It’s true. I was so mad at you, at S.H.I.E.L.D. that I partnered with that bastard. I got that Ward guy to bring Skye to me at Whitehall’s base. If it weren’t for me she never would have even been there. She would have been safe with you.” Cal had tears slipping down his face as he spoke.

“You couldn’t have known what would happen Cal. Either way it doesn’t matter now. The past can’t be changed. What matters now is that we work together to get her out of here. If we get a chance to escape, we take it.” Coulson said, trying to get Cal to focus on what mattered, not to wallow in his guilt.

“Agreed, we have to get her out of here.” As soon as Cal finished speaking the door slammed open, jolting Skye awake causing her to wince as she pulled at the stitches in her neck.

“You haven’t gotten it through your heads yet have you?” Whitehall said with a smile to Cal and Coulson, then he turned his smile on Skye, “She’s not going anywhere.”

Skye shrunk into the table as he stared at her. Coulson and Cal were desperate to keep his attention off of her.

“Why don’t you torture one of us instead huh! She is no different than us!” Cal yelled at Whitehall.

“And that’s the frustrating part Doctor. So far all of my tests seem to agree with you. I haven’t found anything to prove Skye’s specialness to me. When I tortured her mother, I found anomalies in her blood and organs that proved she was not human. She was undoubtedly unique inside. So far there is nothing in Skye’s samples that make me think she has the same uniqueness as her mother.” Whitehall said with a small frown as he looked at Cal.

“See, we told you Skye was not special. There is no reason to keep on hurting her.” Coulson said. Whitehall didn’t seem to hear him, he kept talking to Cal.

“But then I got to thinking. You see when we were leaving the theatre in Puerto Rico I ran into Raina.” Cal’s stomach sank as Whitehall spoke. If he knew that Raina had been changed maybe he knew that Skye could change too. Whitehall continued, “To my surprise, she emerged from the temple a completely different person. Her entire body was covered in thorns, she even used one to slice one of my agent’s throats. She managed to evade capture but before she did she spoke of what had happened in the temple. She told me she knew what was inside the Diviner. She even offered it to me.” As he said this he pulled the crystal out of his pocket.

Cal’s face went white. Coulson was looking between Cal and the crystal trying to understand what was happening. He had no idea what that crystal was but the fact that it had come out of the obelisk coupled with the fear he saw in Cal’s eyes told him it was not going to be good.

“Now I have analyzed a sample of this crystal but there wasn’t much I could determine apart from the fact that it is definitely alien. But what I did discover is that when the sample I took was broken it released a mist. So I started to wonder, Raina changed when she opened the Diviner and came into contact with what was inside. Maybe Skye isn’t special yet but she will be after she is exposed to the mist.” Whitehall continued.

“No, please don’t do this. Not like this.” Cal pleaded.

“Please, she’s too hurt right now just let her rest for a while.” Coulson said, he didn’t know what the crystal would do but it couldn’t be good in Skye’s state.

“Don’t worry gentlemen, I would never risk losing my hostages by exposing them to something that might kill them. You two can stay here, out of danger, while I take Skye to a sealed room. Then we will see just what will happen when this crystal breaks near someone like her.” As Whitehall finished talking the nurses from before entered the room. They disengaged the brakes on Skye’s bed and began to roll her out of the room. Coulson and Cal both started yelling.

“No, Skye! Please don’t do this! Just take me! Don’t hurt her!” Coulson screamed.

“You son of a bitch! Leave her alone! Daisy!” Cal yelled.

Both men were fighting with all their strength against the chains on the wall. Whitehall was watching them with sadistic pleasure. As Skye was being rolled away they could hear her weakly protesting.

“No please don’t! Just take me back to them. Coulson! Dad! Coulson!” Her voice died out as she was wheeled out of sight and deeper into the compound.

“Fear not gentlemen you won’t have to miss anything.” Whitehall gestured to a guard outside the room who wheeled in a tv screen and hooked it up to the wall. Immediately both men’s eyes were glued to the screen as they saw an empty concrete room. Soon enough Skye was wheeled in and left in the middle of the room, the two nurses locking the brakes on the bed and exiting.

“Enjoy the show.” Whitehall said with one last smile at both men before he left the room.

Line Break

“There it is, Whitehall’s lab.” Bakshi said. They had been driving for several hours now and Hunter was relieved they had finally made it.

“So this is where Whitehall would go if he needed to get away in a hurry?” Hunter wanted to be sure they were in the right place before he revealed himself to Bakshi.

“Yes, if what you said is true and things went South in Puerto Rico this is where Dr. Whitehall will be. He would want to regroup and form a new plan.” As Bakshi finished speaking Hunter pulled off the road.

“What the hell are you doing, take me all the way up to the building. What do you expect me to do? Walk from here?” Bakshi was furious as Hunter stopped the car.

“Nope, you won’t be walking anywhere.” Hunter said as he pulled out an ICER and shot Bakshi.

“May that’s the building, a few miles from my position. Bakshi’s iced.” Hunter reported in over comms. As he spoke Agent Romanoff approached the passenger door and put some cuffs on Bakshi’s wrists. She shoved his body into the back seat then climbed in and closed the door.

“Good work, we have found a clearing about 3 miles east of your position that is big enough for us to land in, you two head that way and we will see you in a bit.” May replied.

“Copy.” Natasha responded.

Line Break

“Fitz can you pull up the building specs?” May asked. Clint was in the cockpit landing the plane while everyone one else was in the command center.

“I can get the blueprints but there is no way to know if Hydra has changed the structure.” Fitz replied.

“Jarvis send me a thermal readout of the structure and start satellite surveillance.” Tony said into his comms.

“Of course, sir.” Jarvis voice rang out through the plane. Everyone looked at him.

“It was a long flight, figured I would hook Jarvis into the system.” Tony shrugged. Suddenly they had blueprints, scans, and thermal readings for the building on the screen in front of them.

“Thanks Stark. Alright, it looks like there is a front and back entrance. So, two teams, simultaneous breach. From the thermals it looks like there are about three dozen people inside, spread out throughout the building and three of them are friendlies.” May said. As she spoke Clint came in from the cockpit having successfully landed the plane.

“The front looks like it has the heaviest fortification. Stark, you want to take it?” Steve asked.

“My pleasure.” Tony responded. They all turned as they heard footsteps and saw Hunter and Nat lugging an unconscious Bakshi up the stairs.

“Put him in the cage.” May instructed. They did so, then joined the group in the command center.

“Alright, who’s going in the front with Stark?” May asked. She figured it might be easier to just let everyone divide themselves up rather than trying to assign them to teams herself.

“Clint and I will go in the front.” Nat said.

“I will go in the back.” Steve said.

“I’ll go with the Captain.” Tripp said, he was excited and honored to have a chance to work with the man his grandfather always spoke so highly of.

“Hunter and I will go in the back as well.” Bobbi said after sharing a nod with Hunter.

“Then I will go in with the team in the front. Mack and Fitz will stay here and run back end, monitoring comms and sat surveillance to let us know if anything changes. Simmons and Dr. Banner will be here on standby if anyone needs medical attention.” All four nodded as May spoke.

“Our priority is finding Coulson, Skye, and Skye’s father. Any intel that we can gather is great but don’t get distracted. Take out anyone who gets between us and our people.” May said firmly. There were several “Yep” and “Hell yeah” around the room as well as several nods. May continued, “Alright, let’s go.”

Line Break

May, Clint, Nat, and Tony were crouched in some bushes about 100 yards away from the entrance to the lab building.

“Team 1 is in position. Team 2 what’s your status?” May asked.

“In position.” Steve’s voice responded.

“Alright on my mark Tony is going to blow the doors. In 5, 4, 3, 2… what the hell is happening!” Before she could finish her count the entire building and the ground around it started to shake.

“I don’t know, there seems to be some kind of earthquake... wait it’s stopping.” Fitz said over the comms.

“Ok, let’s go, Stark now!” As she said now Tony stood from his position and sent a missile right into the front door of the building leaving a massive hole in the structure. It took several moments for the agents inside to regroup by which point May, Nat, and Clint had moved in and were coming through the hole with their weapons out. Clint’s arrows started flying while Natasha was shooting widow bites left and right. May took out the few still standing with her ICER. Iron man came in as the dust settled on the dozen or so Hydra agents dead or unconscious on the floor.

“Huh, I don’t think you guys really need me.” Tony said sounding offended.

“Shut up and go search the upper floors Stark.” Nat said.

“Copy that.” Tony said as he blasted off through the ceiling above them leaving a massive hole behind him.

“Fitz?” May questioned.

“Head to the basement, the biggest concentration of heat signatures seems to be down there. Stairs to your right.” Fitz replied.

“Copy.” Clint said and the three moved for the stairs.

Meanwhile team 2 was finishing up their entrance party in the back. Steve had gone in first, taking bullets to the shield before attacking the two agents nearest him. Bobbi had been right behind him attacking the agent that was still firing. As they fought their assailants Tripp and Hunter laid down cover fire, taking out any agents that came running their direction. Soon enough all the Hydra agents were down the four of them also moved to the basement stairs, having heard what Fitz said about the heat signatures down there.

Upon reaching the basement May, Nat, and Clint had all split up and Steve and Tripp had gone off in a team of two while Bobbi and Hunter went off together. Bobbi and Hunter came across some type of Lab full of microscopes, DNA sequencers, and several other types of diagnostic machines. They saw several vials of blood and other human tissue samples and they both had to hold back the fear that shot through them upon realizing the samples might have come from one of their friends.

Tripp and Steve found several scientists trying to escape and iced them but they hadn’t found any of their missing people yet.

Clint took out several more agents and found himself in what appeared to be a security room. There were security monitors with feeds all around the base. He called out to Fitz, “Hey Fitz I’m in the security hub, can I send the feeds to you?”

“Yes, let me talk you through lowering their security so I can hack in.” Fitz said as he coached Clint through the hack. In a few minutes he had eyes on the whole facility.

“I’m in the security system. I know where Coulson and Cal are but I can’t find Skye. May and Romanoff are closest. May if you turn the corner in front of you Romanoff is there then you two can continue on to the others.” Fitz said.

“Fitz I’m in a straight hallway there are no corners near me.” May replied.

“That’s not May.” Simmons said from behind Fitz.

“Agent Romanoff you are about to run into Agent 33!” Fitz yelled into the comms.

“I’ll take her in alive.” Nat said. She charged around the corner and leapt onto Agent 33, stunning her with her widow bites so she collapsed to the floor.

“She’s down.” Nat said.

“Alright, Agent Romanoff, go straight down that hallway and then take a left, Agent May go straight until you reach the fork in your hallway, you two will run into each other… now.” They met as he said now. “Ok, go left at the fork. Stop, open the door on your right.” They did as Fitz instructed and opened the door.

“May!” Coulson said from his spot on the floor.

“Phil.” She breathed out in relief as she and Nat rushed into the room she immediately went to pick the lock on the cuffs around Coulson’s arms as Nat did the same for Cal. As they kept talking the rest of the team found them.

“May, May stop you have to go get Skye!” Phil shouted at her.

“We’ll get her Phil just let me unlock you first!” May said angrily, she needed him to sit still if she was going to unlock him but he kept squirming.

“No, you don’t understand, Whitehall took her! He experimented on her and then he separated her from us and exposed her to some alien thing and then he took her!” Phil was speaking so fast May could barely understand him. The whole team was listening intently to them.

“What do you mean he took her?” May couldn’t focus on anything else he said, she just knew that Skye wasn’t here and now Coulson was saying she was gone again.

“When you attacked Whitehall knocked her out and told his guys to bring her to the plane on the roof.” Phil rushed out.

“How do you know this?” Natasha said from where she had just finished freeing Cal.

“He made us watch on that screen.” Phil said and everyone turned to see the tv screen on the other side of the room. As they were all distracted Cal got up and ran from the room.

“Cal, hold on!” Coulson yelled as he got up and ran after him, the entire team hot on his heels.

Cal ran straight for the stairs to the roof. As soon as he got up there he froze, he didn’t see anything, no plane, no Daisy, nothing. Then suddenly a shot rang out. Cal looked down to see blood blooming on his chest. Coulson burst onto the roof just as Cal collapsed.

“No!” Coulson yelled as the cloaked plane lifted off from the roof and they saw the thrusters disappearing form sight. Coulson went to Cal.

“Tell her I’m sorry. I tried to protect her… You have to save her Phil. Save my girl.” Cal muttered, blood beginning to pour from his mouth.

“I will Cal, I promise.” Coulson said, grabbing Cal’s hand.

“Thanks Phil.” Cal said as he closed his eyes. Breathing his last breath.

Line Break

Once the nurses left Skye alone in the room Dr. Whitehall entered.

“Well Agent Skye, let’s see what you truly are.” He said with a smirk as he put the crystal on a shelf by the door. Skye saw some kind of mechanism above the shelf that she imagined would break the crystal when triggered.

“Please… please don’t do this.” Skye whimpered as tears slipped down her face. Whitehall knelt down by her face and wiped her tears away with his thumb.

“Have faith Skye, maybe the mist will kill you and you can see your mother again.” He smiled and left the room as Skye let out a loud sob. As the door closed Skye was left to stare at the crystal sitting only a few feet away from her. She wondered how long the sick bastard would make her wait before her broke the damn thing. She didn’t have to wait long, after a minute she heard a metallic click and saw a hammer come down on the crystal.

A mist began to spread out from the crystal and come towards her body. She fought against her restraints, struggling to get away but it was too late. The mist engulfed her. For a moment she didn’t feel anything, then suddenly there was a strange crawling feeling under her skin. She craned her head to look down at her body and saw rock coming out of her hands, her hip, climbing all over her. Soon enough it was reaching up her neck. She screamed to no avail as it swallowed her whole.

It was completely dark, she felt nothing but pain, like her body was being ripped apart, then the pain stopped and was replaced with something else. A rumbling under her skin like bees had been trapped inside her. Her whole body felt like it was shaking. Suddenly she heard a crack and saw light peeking through a hole in the rock over her face, she started squirming trying to free herself and slowly the rock fell away from her body. She was hyperventilating, trying to understand what she was feeling, when the door opened and Dr. Whitehall walked in beaming from ear to ear. His eyes scanned her from head to toe before he spoke.

“Skye, I’m so thrilled you survived! Now we get to start all over again!” Whitehall spoke with more glee than Skye had ever heard come from the man. She was confused by his words before she realized her neck didn’t hurt anymore. She looked down and realized her hip and back didn’t hurt anymore either. Whatever had just happened, it had healed the wounds he had inflicted.

She realized that he intended to do his experiments all over again and a new bolt of fear shot through her. As he began to approach her bed the fear increased and she felt her body’s shaking increase except now she wasn’t the only one shaking. Whitehall was shaking too. In fact, the entire room was shaking. Whitehall stumbled back into the wall and looked down at the ground in surprise. He looked up to Skye and said, “So that’s what you are. You’re even more spectacular than your mother.” With a huge smile on his face he carefully walked up to her bed and stroked a hand down her face causing Skye to flinch. Then he pulled a syringe out of his pocket and plunged it into Skye’s neck. The last thing she saw as she fell into unconsciousness was his smiling face.