Theta Protocol

Maria Hill hung up her phone and put her face in her hands. She knew that the whole Whitehall situation was getting bad, but she didn’t see this coming.

Apparently, Coulson had gone into the Hydra stronghold with just five agents to recover a sixth and stop Hydra and gotten himself and an agent captured in the process. Not to mention they failed to stop Hydra from doing whatever it was that they were trying to do.

Now Maria is stuck with the fun task of not only informing the Avengers that Coulson is still alive, but also that he is missing and might be killed if they don’t help his newly rebuilt version of S.H.I.E.L.D. to recover him. Just great.

Maria straightened up, pulled some files off the printer that the Koenigs had sent over, and stepped out of her office in Stark tower. She entered the elevator and asked Jarvis to take her to the command center and ask the Avengers to meet her there as soon as possible.

She only had a few minutes alone in the room before Clint and Natasha came in. They each gave her their own questioning look but when she shook her head they both nodded and took their seats.

Next came Steve and Bruce. Steve was on high alert, “What’s going on Maria? Is something wrong?” Maria replied, “I would prefer to wait for Tony so that I don’t have to repeat anything.” The men both nodded apprehensively and took their own seats at the table.

Then came Tony who blustered in and said, “This better be quick I was in the middle of some important new upgrades for my Iron Legion.” Maria took a deep cleansing breath then replied, “If you could sit down Tony I would like to get started.” Tony shrugged then flopped into his own chair and propped his feet up on the table. He was also nervous about what might be wrong, but nonchalance was his go to coping mechanism.

“Great, now that we are all here I have to start off by apologizing.” That got everyone’s attention on her immediately. Tony perked up and pulled his feet off the table to sit up a bit straighter. “The reason that we kept this from you was not because we didn’t trust you or because we thought you couldn’t handle the truth.” Maria was now making direct eye contact with Natasha and Clint; she knew this would hurt them the most. They would feel completely betrayed, she just prayed they would understand. “Phil Coulson is alive. He did die on the Helicarrier when Loki stabbed him but Fury had doctors who performed some medical miracles to bring him back and ever since then we have been keeping his life a secret.”

A hush fell over the room, no one dared to speak. Maria thought it best to wait before she continued so everyone would have a chance to process the news. Natasha broke the silence, “We went to his funeral.” Her tone was eerily calm and quiet. If the room hadn’t been so silent no one would have even heard her at all. Then Clint chimed in, “We mourned for him for almost 2 years. How could you let us believe he was still dead?”

“We weren’t keeping this a secret because of all of you, it was about protecting Coulson.” Maria said.

“Since when did Coulson need protection from us?” Natasha responded. For those who knew her best, they could hear the hurt in her voice. She always feared that the people she cared for would come to fear her, she just never expected it to be Coulson.

“He needed protection from what was done to him.” Another eerie silence fell over the room, this time Steve was the one to break it, “What do you mean what was done to him?”

“In order to bring him back Fury had a team of doctors who were experimenting with alien DNA inject Coulson with alien blood. The previous subjects who had experienced this treatment had all had terminal illnesses beforehand and the alien blood was able to heal their ailments, fix them. Fury hoped that, since Coulson had only been dead a few days by that point, that maybe the blood could bring him back. And it did.”

“At what cost? What were the side effects?” Bruce spoke up, as a doctor he was simultaneously intrigued and horrified by the idea of using such an experimental treatment on anyone, let alone a man like Coulson. He may not have known Coulson very well before his supposed demise but he seemed like a good man. Everyone at this table spoke of Coulson with such admiration, it made Bruce want to protect him too.

“The test subjects had experienced a wide range of after-effects. Hypergraphia, aphasia, catatonia, and eventually they all ended up in some form of psychosis. We were able to save them, but only by replacing their memories of what had been done to them. We wiped away who they were, gave them new lives, and they were free of the side effects. We had to do the same thing to Coulson to make sure he didn’t suffer the same side effects. We erased his knowledge of the procedure and we sent him to a new team with less danger attached. A team where he could be monitored for side effects and contained if need be. That’s where he was when S.H.I.E.L.D. fell. Running an off-book team from a mobile command unit.”

“So he’s ok? He isn’t experiencing the side effects? Is that why you’re telling us this now? Can we see him for ourselves and make sure he’s ok?” Tony’s mask of indifference was completely gone now. Coulson was someone that he truly cared about. Tony needed to see him, he needed to be sure that this was all true. He had lost a true friend when Phil Coulson died so having him back… He just has to be sure.

“Unfortunately no. I’m telling you this because Coulson has been taken.” “WHAT?” The whole room responded at the same time and they all began clamoring for answers at once. Maria raised her hand to silence them.

“After S.H.I.E.L.D. fell, Fury found Coulson and his team and he gave Coulson a new task. He told Coulson to rebuild S.H.I.E.L.D. For the last year Coulson has been the director of the new S.H.I.E.L.D. He has been rebuilding it, fighting back Hydra, slowly acquiring new agents and resources. They have been taking on Hydra from the shadows. He and I have stayed in contact and we have developed an emergency protocol that Coulson would activate in case things went wrong and they needed Avengers back up. It has been activated.”

“What do we know?” Steve was all strategy now. Any chance to fight Hydra was ok with him. He still had his problems with S.H.I.E.L.D. and what they were before, but he liked Coulson, and maybe with him in charge things would be different this time. They needed to help with this fight and he was ready to do whatever it takes to get Coulson back. In the short time that he knew Coulson, he knew that he liked him. And seeing how everyone reacted to the news of Coulson’s death had just confirmed what a great loss it was. Coulson deserved their help.

“For several months now Coulson has been experiencing hypergraphia from the alien blood in his system. He has been compulsively drawing on the wall of his office and he knew that whatever it was that he was drawing was something that needed to be deciphered. With the help of one of his agents he was able to track down the other former subjects of the experiments and they came to realize that what they were all being compelled to draw was a blueprint of an ancient alien city, hidden underneath the city of San Juan, Puerto Rico. Once Coulson had deciphered the meaning of his carvings, his compulsions were gone and his hypergraphia was cured.”

“Thank God.” Bruce added.

“They have also been trying to stop Hydra from obtaining an alien object of unknown origin, known as the obelisk, with the ability to turn anyone who touches it to stone. Hydra was able to get their hands on the object and Coulson’s team learned that the object and the alien city from Coulson’s drawings were related and Hydra was planning to take that object to the city.” Natasha spoke up, “Why were they taking this obelisk there? Didn’t they already get what they wanted from it, the ability to kill anyone just by touching them?”

“Coulson’s team learned that Hydra had an expert on the obelisk who had told them that the obelisk had some other power within itself that would be unlocked if it was taken to the alien city. Coulson’s team doesn’t know what that power is but they knew that they needed to stop Hydra from activating it. The team went to San Juan and found Hydra’s stronghold. Coulson and several other agents went in to stop Hydra but they were outmanned and Coulson and another one of his agents were taken hostage. I received the call from one of Coulson’s agents 45 minutes ago. Coulson said that if things went South he was to call in the Avengers.”

The team around the table all looked at each other, then Steve spoke, “Tony, how fast can we be in San Juan?” “Wheels up in 5, grab what you need.” Tony replied.

The team all filed out of the room with Maria right behind them. She knew they were all processing a lot and once they joined the S.H.I.E.L.D. agents there would be even more surprises, but for now, they were all on board and ready to join the fight.

Line Break

Natasha couldn’t stop watching Clint. He had been almost completely silent throughout the debrief with Maria. He had not spoken since they got on the plane. She sat down next to him and nudged his shoulder with hers.

“You doing ok?” Natasha asked in a hushed voice.

“Not really. I get that Fury wanted to keep this whole thing a secret, I just can’t believe that Coulson didn’t tell us anyway. If it was me nothing would have stopped me from telling you both that I was still alive, Fury be damned.” Clint replied.
“We still don’t know Coulson’s side of this. I’m sure he had his reasons for keeping this a secret. We won’t know until we get him back. Then we can kick his ass for not telling us and never let him out of our sight again.” Natasha said with a smirk.

“Yeah, sounds good to me.” Clint responds with a huff and a smile. The two fall back into silence. Both are praying they make it to Coulson in time to get the answers they so desperately need.

Line Break

It had been two and a half hours since Coulson and Skye had been taken and May was getting pissed. They hadn’t made any real progress towards finding them. Not to mention they had no idea what Raina had triggered with the obelisk in the tunnels.

“I tracked the SUVs to the airfield. Obviously, Hydra had a plane on standby to get away, but there are no cameras at the airfield beside the ones at the gate so I can’t see what plane they got on or which direction they took off in.” Fitz sounded as frustrated as May felt.

They were all standing around the command center of the Bus except for Simmons and Mack who were downstairs in the Lab where she was running every test she could devise to make sure that he was truly ok. Fitz was hacking security cameras, bank accounts, social media, anything that he could think of to help them track Skye and Coulson. It felt more and more like they were grasping at straws.

“Just keep trying Fitz.” Bobbi said, whilst reassuringly patting him on the back. May gestured to Bobbi, Hunter, and Tripp and the three of them stepped out of the command center into the lounge. May looked at them all, “Update?”

“I called the Koenigs, they are sending more agents and techs. If you give the go ahead when they get here they will go down into the tunnels and try to figure out what Raina actually did down there.” Tripp added.

Hunter continued, “I followed any physical trail that I could to track down Hydra but they all just lead me to the same airfield where Fitz lost them on the cameras. They went into the airfield and didn’t come out. They definitely left in a plane, they’re not in Puerto Rico anymore.” May grimaced.

Bobbi pressed on, “I cuffed and contained all the Hydra agents that were left alive after the fight at the theater. I interrogated the ones that I could but they didn’t seem to know anything about where Whitehall would have gone. None of them are high enough up on the food chain to be told anything of actual importance.” Bobbi paused before she added, “I also found Ward’s dead body.” May looked surprised for a moment and then nodded, “Call General Talbot and tell him that we have some Hydra agents to add to his collection. Don’t tell him anything about Coulson or Skye.” Bobbi nodded.

The three fell quiet. Tripp, Bobbi, and Hunter looked at each other, all three knew May was barely maintaining her calm but they knew there wasn’t anything they could do for her at the moment.

Suddenly Simmons voice came over the Bus’ comms system, “May, would you and the others please come down to the lab. Please.” Simmons voice sounded weirdly strained, like she was feigning calm. May and Bobbi shared a quick, anxious glance then both bolted for the stairs followed closely by Hunter, Tripp, and Fitz.

As May got to the top of the spiral staircase leading to the ramp she saw what had made Simmons sound so strange. Maria Hill was standing on the ramp with 5 Avengers at her side. May walked calmly to the bottom of the stairs and threw a quick nod to Simmons to reassure her that everything was ok, then she walked right up to stand in front of Natasha.

“Bù zhīdào shì wǒ jiàn dào nǐ gèng chījīng háishì nǐ jiàn dào wǒ gèng chījīng” (I am not sure if I am more surprised to see you or if you are more surprised to see me?) May said. Natasha smirked and responded, “Juéduì shì wǒ” (definitely me.) Then her face turned serious and she looked May firmly in the eyes, “Wǒmen huì bǎ tā zhǎo huí lái” (We will get him back.) May nodded at her then turned to address the whole group.

“I guess Coulson had a safety measure that I didn’t know about,” May said. Maria responded, “Once the shit hit the fan here, Koenig called me and activated theta protocol, to bring in the Avengers.” May’s eyes scanned over the whole team, then she said, “Let’s take this upstairs.” She turned and marched back up the way she came.

Maria immediately followed May up the stairs, throwing a smile at Bobbi as she passed her. Tony and Bruce looked at each other, not sure if they were impressed or intimidated, and then followed Maria. Bobbi smiled at Natasha and Clint then hugged them both saying, “Long time no see.” Nat just smiled at her while Clint threw an arm around her shoulders and the three began to walk up the stairs together. Hunter glared at Clint’s back while he followed after them and Tripp shook his head at Hunter then followed him. Steve took up the rear of the Avengers group after throwing polite nods to Fitzsimmons and Mack. Fitzsimmons waited until all the Avengers were out of eyesight of them and then immediately began freaking out and talking to each other in a rapid fire, hushed way that had Mack rolling his eyes. He just said, “Come on then.” And led Fitzsimmons up the staircase to join the rest of the party.

Once the group had all crowded into the command center, May began to speak. “So what do you all know?” Maria responded, “Koenig sent over some files and I gave these guys the overview, of Coulson’s condition and how that lead us here, and about Hydra’s mission. I told them that Coulson had been taken and then we were all equally motivated to get here and figure out everything else.” “And what about Skye?” May’s eyes flashed angrily. She didn’t like that Skye seemed to be an afterthought to this new group. She knows that Coulson is the common thread amongst all the people assembled before her, but Skye is just as important.

“I didn’t have a chance to get into any of Skye’s involvement or history.” May exhaled through her nose and gave a curt nod. She began her own summation of the case. “Skye was also taken by Hydra. I believe that they also took her father but he could have gone with them willingly.” “Hang on, this girl’s father would cooperate with Hydra like that.” Tony’s tone was not impressing May but once again she pushed aside her feelings. “Yes, he has been working with Hydra but we believe he has been working with them only out of a desire to accomplish his own goals, not because he believes in their cause.”

“So what is his goal then?” Natasha sensed May’s anger and anxiety roiling under the surface, she wanted to pull her aside right then and there to ask her what was going on but she had to get through this first. She figured that it would help if she took over asking the questions instead of letting Tony keep doing it. “He wants Skye. She was taken from her parents when she was a baby.” “Who took her?” Clint spoke up. “Hydra.” May responded. They had no official confirmation that it was Hydra who had sent agents into that village in Hunan to get baby Skye but she and Coulson were sure.

“When she was a few months old, Skye’s village in China was attacked by Hydra. All the villagers died trying to protect her. When S.H.I.E.L.D. agents were sent in to find her they were told that they were looking for an 0-8-4, an object of unknown origin, instead what they found was a baby girl covered in blood, asleep in a dead agent’s arms.” May paused to let the horror sink in with everyone. She needed them to take this seriously. Hydra had been trying to get their hands on Skye since she was an infant and they finally had her. May shuddered to think of what they might have planned for her now.

“The team who recovered her and brought her back to the states started to get tortured and crossed off one at a time by someone who was trying to find the baby. The last two agents left alive realized that the only way to keep the baby safe was to hide her so they dropped her off on an orphanage doorstep and created a level 8 invisible protocol that ordered the foster system to move the baby around every few months. It kept her safe from whatever was hunting her. On our first mission as a team we picked up Skye as part of an investigation and brought her onto our team as our computer specialist. She began to train to become an agent.

“There was a woman that we had encountered in our investigations of Hydra before S.H.I.E.L.D.’s fall, Raina, and she contacted us several months ago. She tried to blackmail Coulson to get him to let Skye go with her. She said that she was going to take Skye to meet her dad. When Coulson refused she gave us Skye’s father’s location. By the time we got there he was long gone. Sometime after that he took the obelisk, which he had in his possession, and gave it to Daniel Whitehall, one of the heads of Hydra. He told Whitehall all that he knew about the obelisk and that there was something inside the obelisk that would be activated if you take it to the temple inside the alien city. Coulson, Fitz, and Tripp were on a mission to map the earth and find the location of the alien city when they ran into Skye’s father. This is when he revealed that he was working with Hydra since he blamed S.H.I.E.L.D. for losing Skye as a baby.”

“Soon after that we learned that Hydra was trying to abduct Raina so we took her into custody where she revealed to Skye that she is able to hold the obelisk and she is supposed to carry it into the temple and be the one to activate it. Hydra managed to track us through Raina and they sent a team to get her from us. That team was led by a former team member of ours who was revealed to be a member of Hydra during S.H.I.E.L.D.’s fall. He has since become obsessed with Skye, believing that he is in love with her. When he came to take Raina from us he also took Skye. When we all regrouped here in San Juan we were able to find Hydra’s location, at the theater Ponce de Leon and Coulson, Bobbi, Hunter, Tripp, and I went in to stop Hydra and find Skye.”

“Where were you during all of this? I mean no offense but it seems like you should have been in there kicking ass with them. You’re kind of huge.” Tony said looking at Mack. Mack grimaced and stared at the table in front of him while he spoke. “When we first got to San Juan I went down into the tunnels of the alien city to scout them out. When I touched the floors of the city something came over. I was being mind controlled by the damn thing. I attacked my team, nearly killed Bobbi. They had to throw me back down into the city and seal me in. I was down there, stuck inside my own head until Raina did whatever she did to activate the obelisk. When she went into the temple, the mind control freed me and I was able to get back to the team.” They whole room went silent. Tony looked like he had been slapped. Natasha recovered first and said, “Wait, so Hydra did whatever they were trying to do. Raina activated the obelisk?”

“Yes, but we still don’t know what it did. She must have slipped down into the city during all the commotion in the theater. Tripp and I were searching for Skye when we heard several engines and we ran out onto a loading dock just in time to see Skye and Coulson being put into a couple of SUVs and then they were gone.”

Fitz spoke up, “I have tracked Hydra to an airfield nearby where they must have boarded a plane. I can’t find anything on them now.”

May glanced around the room, then spoke, “I have more agents and lab technicians coming to determine what Raina did in that city, Simmons you should stay behind and supervise them, Tripp you will stay with her and watch her back. The rest of us should head back to base and regroup. We can start hunting down Whitehall’s location from there.” “I’d like to stay behind with the team who is investigating the city.” Bruce chimed in, then added, “Another scientist helping can’t be a bad thing.” May nodded at Bruce, she wasn’t going to say no to an Avenger offering assistance. “Alright, Tripp, Bruce, and Simmons will stay behind and figure out what Raina might have been up to in the city. I will leave the quinjet with you. Once the three of you are done here return to base.” Tripp nodded in confirmation. May turned to Maria, “Did you fly here in a quinjet?” “Yes” Maria confirmed. “Then dock it on the Bus and we can get going. Wheels up in 5.”

As everyone started to disperse May went over to Fitzsimmons, “I need to see you both in the lab.” The three made their way down to the lab where May closed all the doors to ensure they had privacy. She turned and looked at Fitzsimmons before taking a deep breath. “Ward is dead. Bobbi found his body in the theater. He’s dead. I wanted you both to hear it from me.” No one said anything, the three just looked at each other for a long moment, then May gave them each a nod before turning and leaving the room.

Simmons turned to Fitz and grabbed his hand. “He’s gone.” Fitz looked in Jemma’s eyes and smiled. He wrapped his arms around her, she clung to him tightly in return. Fitz echoed Jemma’s thoughts, “He’s gone.”

Line Break

Coulson felt so stiff, like he had fallen asleep in a weird position. He slowly sat up and opened his eyes. He looked at his hands and saw that they were cuffed to a chain which was secured to a loop in the wall by his head. He was sitting awkwardly on a concrete floor. He noticed another body next to his, with their hands cuffed and chained to another loop in the wall just like Coulson’s. Coulson peered at their face and realized it was Skye’s father.

His memories rushed back to him. Cal had been shot twice and knocked unconscious. Coulson was captured too. He remembers putting pressure on Cal’s wounds and worrying about how much blood he was losing. He noticed that Cal’s injuries have been tended to and wrapped in white bandages. Coulson remembers being pulled to his feet then someone was yelling. Skye. Oh God Skye. His eyes frantically search the room and his blood runs cold when he sees her. She’s lying on a table several feet away from him. Her hands and feet are strapped to the table and her body was covered by a thin white sheet. She doesn’t appear to have any clothes on. It was then that Coulson noticed all the medical equipment around the room. IV stands, surgical lights, and trays full of medical tools.

To his left, Cal begins to stir. He comes to slowly and with several grunts of pain. As he sits up his eyes meet Coulson’s. “What happened? Where the hell am I?” Coulson has no answers for him but he figures he should try to keep him calm. “I don’t know where we are but as for what happened, I can tell you that Whitehall shot you, in your shoulder and leg, and then he knocked you unconscious. I was captured while I was trying to rescue you.” Coulson gives Cal a moment to process. Then Cal’s head turns and he sees Skye.

“Daisy. Oh no. Oh my God. My Daisy. No this can’t be happening. This can’t happen. I won’t let him do this to you.”

“But how are you going to stop me?” Whitehall spoke from the doorway with that sadistic smile on his face. Coulson had seen him enter but Cal had been too swept up in the emotion of seeing his daughter strapped down to a table the way his wife had been. Cal turned to Whitehall.

“You monster! You can’t do this! You already took her mother from me! I won’t let you take Daisy too!”

“But I made you a promise doctor. I told you I wanted you to watch what I did to your daughter.”

At that moment, Skye’s eyes opened. All three men froze. Skye turns her head and locks eyes with Coulson. “Coulson, what’s happening?” Coulson doesn’t have a chance to answer or reassure her before Whitehall steps between them and smiles down at Skye.

“Oh good, you’re awake! Let’s begin.”