A/N: Thank you to everyone who followed, favorited and left comments, it means a lot to know people are liking this story.

Feedback is always appreciated. If anyone has any suggestion on how I get this story plot wise and in my way of writing I'm happy to hear it.

Also, I'm sorry it took so long to update but I had some trouble with the brainwash scene and I still don't really like how it turned out.

Disclaimer: I don't own Marvel's Agents of S.H.I.E.L.D..

The ride back to the base was made in silence after Jemma's sobs had eventually quieted down. Everyone was still in shock and no one could believe what had happened. No one could believe that Skye was gone just like that. Skye of all people. She always had such a strong presence and now she was just gone, leaving a hole in the team. How could they move forward? How would they be able to cope with it? Things would never be the same again without Skye around. But they had to keep trying to take down hydra if anything to get justice for Skye.

When they arrived to the base a moment later, they got agent 33 out of the van and put her in a vault so they could assess her situation before interrogating her and trying to start helping her when she woke up.

After that they all went to the playground's conference room to the debrief, all of them still shaken up by what happened on the mission.

"I know we're all still in shock by what happened on the mission, I still can't believe it myself, but we have to keep going. We need to keep going after Hydra and take them down. To get justice for Skye. Make sure her death wasn't for nothing." Coulson said when everyone was there.

Fitz shook his head.

"We don't even know if she's really dead. We didn't see the body. We have no proof that she is dead so she could still be alive." He said not wanting to believe his friend was really dead.

"Fitz" Coulson sighed "There's no way she could have survived that explosion. We have to accept what happened."

"We don't actually know that for sure, sir." Jemma spoke up backing up her friend "I mean, we never even found out the extents of her abilities or even if she had more than one. She could have survived thanks to them."

"It's still a long shot, Jemma." Coulson tried to reason with them in a sad tone not letting himself believe in something that may not actually happen.

"If I could just go back there, maybe I could analyze the bodies and find out if any of them belongs to Skye. And even if it is her, we could bring the body and have a funeral." Jemma suggested hoping that her friend was somehow still alive even though she knew the chances of that happening where slim.

"I don't think it's safe to go back there." Coulson replied.

"Why not? Hydra must have cleaned out before the explosion. The only people there left are the ones that were expendable to them and I'm pretty sure they're long dead." Ward spoke up trying to reason with him.

"Ok." Coulson relented turning to Simmons "You and Fitz can go back and analyze the place. May and Hunter will go with you just in case you encounter someone unexpected."

"Yes, sir. We'll just go get our equipment and then we'll go." Jemma said before leaving the room to go to the lab with Fitz following right behind her.

"And the rest of us, sir? What do we do in the mean time?" Ward asked.

"Agent 33 must be waking up soon. I would like you to go and try to interrogate her." He said before turning to Bobbi. "Agent Morse, I would like you to try and interrogate Bakshi again. See if he may know who the new leader of Hydra is and where their new base of operations may be."

They both nodded in confirmation before they both went their separate ways.

Bobbi went down to Vault D to interrogate Bakshi hoping that this time she would manage to get the intel they needed to stop Hydra and hoping that this time he would be more cooperative.

When she got down there he was lying in the cot placed in the corner of the room but got up when he heard her come down the stairs.

"Back already?" He asked sarcastically.

"You didn't really gave me the information we needed last time so..." Bobbi trailed off sitting down on the chair across from him.

"And I'm not gonna give you anything. So your trip down here was waste of time." he said sitting up.

"I don't get it. How can you be so loyal to Hydra? I mean, they couldn't even bothered to come for you." She replied in disbelief, not understanding how he could be so loyal to someone who just abandoned him like that.

"Is that supposed to convince me to tell you everything you need?" He asked her in a mocking tone.

"I'm just saying, maybe you're not as important to Hydra as we thought or even as you thought you were."

"Then maybe you shouldn't be interrogating me, since I don't matter."

"Nice try. But you still have intel that we need. So you should start talking. You can start by telling me who might be the new head of Hydra."

"New head?" Bakshi asked, confused.

"Yeah. Did I forget to tell you? Whitehall is dead." She said faking confusion.

"That's funny." He said with a dry laugh.

"I'm not joking. Coulson put a bullet in his head. I saw the body myself."

"That's not what I meant. What I meant was that it's funny that you think he's dead. That a simple bullet would be able to stop him."

"What do you mean by that? Whitehall is alive?" She asked, confused.

"Indeed. Doctor Whitehall is not an easy man to kill. He has certain... abilities and can heal better than others do."

"How can he do that?"

"Perhaps you should ask Agent Skye."

"Skye?" She asked, "How could she know about that? What does Skye have to do with Whitehall?"

"Not her. Her mother."

"Her mother?" She asked again, still confused before it dawned on her "Her mother had powers like her. What did Whitehall do to her? Did he kill her?"

"He did, but before that he did something much worse. He opened her up, tore her apart."

"And why did he do that? Besides his perverted way of thinking."

"Discovery requires experimentation." He replied simply.

"Cut the Hydra crap and answer my question."

"He did it so he, let's say, could restore himself. He cut her open and transplanted some of her organs into himself. Consequently he obtained the same powers as her."

"What powers exactly?"

"She didn't age and she healed more easily than normal people do."

"So he gained her abilities?"

"Indeed." He nodded.

"Well, thank you for telling me all we needed to know. Looks like you told me everything I wanted to know after all."

And then she got up heading up the stairs going to Coulson's office to tell him everything she had learned hoping it would be helpful to get Whitehall.

Meanwhile Ward was in another vault where they had locked agent 33 up and was waiting for her to wake up so he could assess the situation so they could decide how to proceed and what was the best way to help her.

He knew that locking her up wasn't the best way to convey their intentions but they didn't know how she would react when she woke up so they had no other choice.

The vault was similar to Vault D where he had been locked up and where Bakshi was now locked up.

Agent 33 was laying on the cot in the corner of the room while he sat in front of the cell wall.

He couldn't stop thinking about what had happened in the mission. He still couldn't believe that Skye was really gone. And couldn't stop thinking that maybe it was his fault. After all, if he hadn't left her behind and helped her fight those Hydra agents she might still be there with them. Fitz and Simmons still hope that she was alive but he just couldn't. He couldn't let himself hope like that. He rather face the reality now.

And that reality was that Skye was gone. They would never see her again. He would never hear her voice or talk with her again. He would never be able to tell her how he really felt. Because despite everything that happened he had never stopped loving her, he just never had the courage to tell her, and now he never would.

He was pulled out of his thoughts by a groan coming from in front of him. Looking up he saw that Agent 33 was awake and was sitting up on the bed.

She looked around taking in the room before her eyes settled on him.

"Where am I?" She asked in a panicked tone.

"Agent 33." Ward started getting up from the chair and walking closer to the laser grid, "I'm Agent Grant Ward. You're in S.H.I.E.L.D.'s custody."

"S.H.I.E.L.D.? No it can't be. He's gonna kill me." She murmured the last part to herself.

"Who? The man you get your orders from? Who is he?"

"You might as well kill me already because I'm not gonna give you anything." She said instead of answering his questions.

"We're not gonna kill you, we just want to help you."

"I don't need your help."

"I know it's hard to believe, but you were once a S.H.I.E.L.D. agent and I like to believed you can still be one, if you let us help you."

"What? No, I was never loyal to S.H.I.E.L.D., I'm loyal to hydra and to Doctor Whitehall."

"Wait, Whitehall? That's impossible, he's dead."

"He's not dead. I receive my orders directly from him."

"So he's the one who..." he trailed off before muttering to himself "I have to tell Coulson."

And then he was bolting up the stairs going straight to Coulson's office and entered, not even bothering to knock.

"Sir, I know who's leading Hydra."

"Whitehall." Coulson said nodding in confirmation.

Only then did Ward looked around noticing Bobbi was also in the room.

"Bakshi pretty much told me everything we needed to know." She clarified.

"So what do we do? How do we get him?" Ward asked.

"First we wait for FitzSimmons to return. If Skye is in fact alive then we'll still have some time to rescue her before it's too late, if Whitehall plans to do what agent Morse think he does."

"What's your theory?" he asked her turning his attention to her.

And then Bobbi started to explain what she thought Whitehall wanted to do with Skye, from the conversation she had with Bakshi.

The first thing Skye noticed when she regained consciousness was that both her wrists and legs were cuffed up to something and even head was being held in place. She tried to move her wrist to see if she could get free but it was to no use since the restraints were too tight. She kept her eyes closed all the while and tried to not move too much so if there was someone in the room she wouldn't alert them on being awake. She tried to listen for any sound to find out if anyone was there and when she heard no sound she opened her eyes looking around the room, taking it all in and seeing if there was any way she could escape finding it to be impossible.

A moment later she heard the door to the room open but before she could fake still being unconscious someone spoke up letting her know they knew she was conscious.

"I see you're finally awake." She heard, recognizing the male voice but being able to remember who it belonged to.

But before she could put a name to the voice the man stepped into her line of vision making her gasp in shock.

She couldn't believe what she was seeing. She thought he was dead and he was supposed to be dead. She saw his dead body. It wasn't possible.

"That's impossible. You were dead." She said in disbelief.

"Maybe Agent Coulson should check twice before assuming someone is dead." He replied, sarcastically.

"He put a bullet through your head. You should be dead."

"Let's just say that your mother's ability help a lot with that." He said, smugly.

"Is that why you kidnapped me? You're gonna do to me what you did you her?" She asked, knowing well what he had done to her mother thanks to her father's disturbing description of it.

"At first that was what I planned to do, but then I saw your abilities and I realized that you would be of more use to me alive, working in the field."

"I would rather die before working for you or Hydra." Skye spat out angrily.

"Oh, believe me. In time you will." He said with a knowing smile, "And you will become a valuable member of our organization."

He then turned away from her and said "Let's get started, I have a feeling we'll be here for a while."

Then, a monitor was turned up in front of her drawing her attention.

Whitehall came closer to her and said in an almost soothing tone "Surrender and you will find meaning. Take a deep breath and calm your mind. Your compliance will be rewarded."

She could feel herself slipping away but she tried to resist the best she could. She thought about the team knowing that they would do everything they could to get her back and that soon it would all be over.

"Are you ready to comply, Agent Skye?" He asked a moment later.

"Screw you." she spat out.

"I knew it wouldn't be easy. But don't worry, we have plenty of time." He told her and stepped away a little.

She doesn't know how much time passes after that. But as it passes, with him spilling Hydra's mottos and beliefs, she can feel herself slipping away no matter how much she tries to resist. And she knows that it's not worth it so she gives up giving into that state of hypnosis until she can't take it anymore and loses consciousness.

She doesn't remember anything before this moment, as she wakes up on a bed of what she assumes is a hospital room. She sits up and looks around taking in the room she's in. She concludes then that she's not really in a hospital but it's clear that she's in some sort of medical bay, of what she doesn't know.

She also can't remember anything prior to waking up and worse, who she is which is a little troubling, to say the least. Had she lost her memories in an accident of some sort? Why wasn't she in a hospital then? Who had brought her there? All those questions and she had no one to answer them.

A moment later though, a man walked in to the room with a triumphant look on his face.

"Who are you? Where am I? Why am I here?" She asked in one breath before he could say anything.

"I'm doctor Whitehall." He introduced himself calmly before asking, "What do you remember, exactly?"

She frowned at the question before answering "Nothing. I don't even remember who I am. What happened? Did I get in some kind of accident?"

"You can say that." He replied.

"What do you want from me?" She asked, starting to get alarmed.

"Just calm down." He said taking a step forward, "Take a deep breath and clear your mind."

She did as she was told knowing it would do her no good to get worked up.

"Good. That's it." He said in soothing tone, "Your compliance will be rewarded."

She felt like something clicked in her brain at those words. It was like all the questions she had before didn't matter anymore.

"Are you ready to comply?" He asked a moment later, seeing a change in her expression.

"Yes, sir." She replied without a second thought.

"Good. There's a change of clothes for you. Get dressed and then meet me in my office. I want you to get started as soon as possible."

"Happy to comply."