AN.1: Hey! So, 3 years and 100 chapters... wow. This is all thanks to you guys and your support. And, as always MegaDiary123. I know I haven't been great with updates, so sorry about that. This is the last chapter of Book 2. I will leave this AN short and say more at the end. I hope you all enjoy this chapter :)

All rights go to Marvel

Clint's POV

Waiting for Skye to wake up was nerve-wracking. Bruce had let me know that she was alright and that we just had to wait for her to wake up from her anaesthesia, but it didn't make me worry any less.

Jemma and Pepper had gone into the room, and I did not want to overcrowd the room or to make Jemma feel pressured. She seemed to have a lot on her plate, there was no need to add any more to it. But she also looked very tired. I had spoken with her a handful of times in the past, especially when I was training Skye, but it had been a couple of good years since I last spoke to the scientist. That didn't discourage Skye from talking about her a lot, so I felt like I still knew her pretty well.

I was in the vents, feeling better at watching the situation unfold from higher up. I had tried contacting Natasha again, but no luck there so far. Maria had also called a couple of times letting me know that she and Fury would be coming in as soon as they could. Probably within the next few hours.

So, there I was, sitting and waiting, watching Pepper and Jemma talk. I noticed how the younger girl would nod off but would jolt herself awake and look at Skye. I let out a sigh and climbed down. Gently, I knocked on the door and peeked inside.

"Oh, Clint," Pepper said and immediately stood up. "Any news on Natasha?" She asked.

I shook my head. "No, nothing yet" I had fully walked into the room. My eyes turned to Jemma. "Why don't you go get some rest? In a proper bed?" I said but saw her tired eyes travel to Skye's form once more. She clenched her jaw like she was stopping herself from talking back and let out a heavy breath. I then realised that my words must have come out harsher than I intended. "You can stay if you want" I added as soon as I made the realisation. "I just meant that you need to get some rest. When was the last time you slept?"

Her free hand went to rub her eyes. "I don't know," she said after a long moment. "I just, I can't leave her," she said, her eyes brimming with tears. "What if she wakes up, or what if something happens?", I could hear a small tinge of panic behind her questions.

"Nothing's gonna happen to her," Pepper said from across the room and then went to Jemma's side placing a comforting hand on her shoulder. "She's alright, we're in one of the most well-equipped buildings in the world. And if anything comes up, Bruce is on standby". There was still some hesitation behind her eyes, though her resilience was wavering.

"You wouldn't be of any use to her if you can barely function" I added gently, trying to reason with her even more. "We promise, we won't let anything happen to her," I said the last part with conviction and her defeated sigh was enough of an indication that she had given in.

She nodded and moved closer to Skye, brushing a strand of hair behind her ears as she whispered something. The quiet of the room didn't really help her in concealing the words and I felt the corners of my lips tilt upwards as I tried to hide the smile that was spreading on my face. She placed a kiss on her forehead and stepped back, letting go of Skye's hand for the first time in hours.

Pepper put her hand around her shoulder, pulling her out of the room and guiding her to Skye's floor. Our eyes met and she nodded at me, mouthing a silent thank you as she led Jemma away.

I turned back to Skye, not moving from my spot.

It was hard seeing her like that.

Skye was a lively and very active person. Not the pale, very still silhouette that was lying on the bed in front of me. Were it not for the heart monitor and the small lift and drop of her chest, there would be no other indication of life whatsoever.

It hurt more than I could admit. Knowing that there is nothing else I can do but wait.

So I moved to where Jemma was sitting before, grasping Skye's hand in both of mine. "Come on, Kid" I whispered. "You are stronger than that. I need you to wake up, alright". My forehead was resting on our linked hands, as my eyes closed and I let the beats of her heart be the only sound in the room.

"Thank you for the help back there," Pepper said as she came back into the room. I had lost track of time, and only her voice brought me back to the present. "Sorry, I knew you must have wanted a moment, but I couldn't keep myself away from her any longer" she apologised as she took her seat across the room.

"No problem, I could tell she was only awake from sheer willpower. How's Stark?"

She let her shoulders slump and relax as she started brushing the back of Skye's other hand. "You know him. His coping mechanism to anything emotional is to go to his workshop and tinker away. I don't know what he started working on this time"

And I honestly don't have the energy to deal with that right now, is what she didn't say but was silently added. I nodded, as I knew the feeling. Natasha would have been at the gym, destroying the equipment, and I probably would have joined her. Both to make sure that she was alright but to also redirect some of the restless energy that was swirling within me. But, now this was where I needed to be, so here I was instead.

"It's been a long day, try and get some rest. I'll wake you if anything changes" I offered in return.

She just smiled softly and closed her eyes. Her fingers soon slowing down their gentle caress until they stilled completely and her breath had evened out.

I let the heart monitor sound lull me in a haze as I was willing the time to pass. At some point, that haze was disrupted from a small twinge of fingers from the hand that I was holding. My eyes immediately travelled to Skye's face, where I saw that her eyebrows were slightly pushed together. "Pepper" I called and she didn't need anything more before she was fully alert. Her eyes travelled to where I was looking and saw the same barely noticeable movement.

"Come on, Skye," I said as I hovered even closer to the girl. I watched as her eyes, still shut, closed and relaxed a few times before she started slowly opening them and blinking. "That's it," I said again as her fingers moved once more in my hand.

In the background, I heard Pepper asking J.A.R.V.I.S. to let the others know that Skye was waking up, but I didn't pay any attention to them, all my focus was on the girl herself.

"Coulson?" She asked when her eyes travelled to my form, her voice coming out hoarse.

I smiled gently, caressing her head. "Your other Old Guy" I corrected. "Clint"

I could see that she was still not really processing anything, and Pepper did too, as she gripped Skye's hand harder to make her shift her attention to her. As soon as her eyes landed on Pepper some more clarity filled them. "Mom?" She quietly asked.

Pepper paused only for a second before leaning in and placing a kiss on her forehead. "Hey, sweetie. You need to stop scaring me like that"

"Where am— Where is— Wha—?" Confusion filled her words as her eyes travelled all around the room. Then, her eyes opened a bit more, as if realising something. "Jemma, is she— is everyone okay? I need to—" she made a move to lift herself off the bed but I quickly pushed her back on the bed. I was not fast enough, however, as she let out a painful grunt.

"Hey, hey, take it easy" I tried to coax her as I heard a commotion from outside the room. "You're okay" was all I could say as her expression was still tight from the pain. I looked up at Banner as the door opened, Jemma following close behind, and he nodded at me.

I tightened my jaw, knowing that I needed to leave the room and let them attend to Skye. Not that I liked the idea one bit. "I'll be right outside," I told her, not even knowing how much she was processing, as I strode out of the room.

Pepper soon followed after a brief talk with the doctors but my attention was on the girl on the bed, pacing back and forth trying to make time pass so that I'd be able to be by her side once more.

Jemma's POV

Soon after agent Barton and Pepper convinced me to go and lay down, J.A.R.V.I.S.' voice filled the room that I was staying in, and I found my adrenaline rushing through my veins. Dr. Banner was in the same elevator as me, as we headed a few floors down to where Skye was.

I could feel my heartbeat in my throat, hoping that everything was alright. My leg's tapping increasing the closer we got to our destination.

The moment the doors opened I bolted, following Dr. Banner closely behind. The moment we walked into the room, Skye was my only concern. I noticed her eyes tightly closed and her eyebrows knitted together. I immediately looked at the machines around the room, taking note of her heart rate and other information. I listened to Pepper as she explained what has happened so far and then she left, clearing the room for myself and Dr. Banner.

I sat by her side, taking her hand in mine. "Skye?" I spoke softly. "Can you open your eyes for me? You are okay, everyone's okay" I tried to reassure her but simultaneously prompt her to look at me. "Come on, Skye, you can do it"

Her head tilted in my direction, her eyes opening ever so slightly. Her gaze met mine, and I smiled. "Jem?" She asked, her voice hoarse as she squeezed my hand and I felt immense relief wash over me.

"Hey, there," I said, squeezing back. "You are okay, everyone is okay. We are at the Avengers Tower" I attempted to explain.

She closed her eyes for a bit, letting out a breath. I could tell that she was trying to work out what I was saying, her brain still a bit confused from the pain medication and the fact that she just came to after surgery.

I noticed Dr. Banner adjusting her IV line nodding at me, not really being bothered that Skye hadn't acknowledged or even seen him. "How are you feeling? Are you in pain?" I asked though I knew the answer.

"He knew", she said instead of answering. Her head lulled to the side, her eyes opening once more, more clarity to them than before. "He knew, Jemma, he knew. How did he know?" She repeated again and again. I could tell that she was becoming upset and agitated as she started moving around a bit as if trying to sit up.

Dr. Banner, who was on her other side, placed a hand on her shoulder to keep her down, as I helped from the other side. As if just then realising that there was another person in the room, she turned towards that person confused. "Bruce?" She asked. "What are you doing here?"

He just smiled kindly down at her. "Take it easy, okay? You are at the Tower. Tony brought you here, both of you" his eyes travelled up to meet mine as he nodded towards my direction. He waited for a response patiently.

"In the Tower?" She asked and when Dr. Banner nodded she turned to me for confirmation as well. "Where are the others?" Her attention was once more on me.

I shook my head. "I don't know. Agent May just said that you were coming here and I refused to let you come alone" I answered honestly. "Now, you need to actually answer me this time, okay?" I said seriously since she was becoming quite aware of her surroundings and was properly awake at this point. "How are you feeling? Are you experiencing any pain or discomfort?"

"No, no I am fine," she said too quickly for me to believe her. Especially when she flinched when she moved about the bed. "It's just, can I sit up? Lift the bed or something?" She asked.

"You are not 'fine' and we both know it," I told her. "Your stomach is quite tender so we need to be careful when we lift you. So, for once, don't be brave and tell me if anything feels off or painful, okay? I had enough of seeing you in pain for a long time" I basically begged her and looked at her softly hoping she wouldn't say no.

I could see her expression soften. And she nodded. As we adjusted the bed I could see her grit her teeth and holding her breath a few time, at which points we stopped until she gave the okay again. By the time we finished there was a very thin layer of sweet on her forehead. "There are a few people that would like to say hi. Do you think you'd be up for that? No-one will hold it against you if you can't"

Her eyes travelled to the transparent walls, for the first time taking in the others waiting outside. She smiled and, even if it was a small and tired smile, I knew she would say yes. She looked at me and her eyes said it all. "Okay, then. You should only see a couple of people at a time, so you don't overexert yourself"

I made a move to leave the room but her hand gripped mine tighter. "Stay" she got out and I did not have the strength to say no, as a huge part of me wanted to stay in the room as well.

"I will let the others know," Dr. Banner said from the other side, smiling at us. He grasped Skye's shoulder and gave her a small squeeze. "I know she won't let anything happen, but if you need anything I'll stay close by"

Skye smiled at him. "Thank you, Bruce. I really appreciate it. Can I have a minute with Jemma first?"

I sat back on the chair that I was occupying a few hours ago as Dr. Banner smiled and left the room. I turned my complete attention to her. "Sorry to have worried you," she said. "Didn't mean to get shot" she almost looked scared at my reaction, like I was going to yell at her or something.

But when had I ever done that? "I know you didn't" I answered softly, trying to let her know it was okay. Even though I had been worried sick, that I had to make sure to keep her alive until we reached the hospital and that I had to wash her blood off my hands. "And you know that I will always worry. But don't think you can escape that easily. I will have you glued on that bed until I am more than sure that you are okay. Don't even think about missions and exerting yourself for a very long time"

She smiled tiredly at me. "Wouldn't dream of it"

I bent down and kissed her on the forehead. "Come on. People want to see you" I smiled back and waited for her to turn to the others and nod.

I was content staying in that chair, our hands linked, as she spoke with her family.

Skye's POV

The next time I woke up, it was to voices arguing outside my room. I came too slowly, to muffled voices that were close, but not too close. The weight on my left hand was still there, which meant that Jemma was there.

Blinking against the light, I tilted my head to see Jemma look out of the room and towards the commission. I shifted my gaze to see what was going on, only to be met with Fury and Natasha having a very heated discussion. Maria was standing on the side, hand rubbing her eyes as she listened to the whole thing, probably trying to find a way to make them stop shouting at each other.

I squeezed my hand, making Jemma realise that I am up, as I turned back to her. "How long have they been at it?" I asked.

She sighed heavily. "A while. Agent Romanoff came soon after you went back to sleep, followed by Steve Rogers. She was waiting for you to wake up, but then the Director and Deputy Director joined us. From what I managed to piece together, he wanted to speak to you immediately and then agent Romanoff started drilling in him about you needing your rest and how you should not be bothered" she explained the whole situation without me having to ask. She knew I would want to know what was going on.

"Well, I'm already up," I said. Looking closer to her, I noticed how tired she looked. "Jemma…" I dragged out. "Have you slept at all?

"Yes," she replied quickly. Too quickly. She saw it on my face that I didn't believe her and she let out a breath. "I got, maybe a couple of hours of sleep? Pepper showed me to your floor at some point, but it wasn't long before you woke up"

She had averted her gaze by the time she finished talking, looking at her lap instead. She was close enough that I could lift my hand and turn her chin in my direction so that I had her attention. "Get some rest, please? For me? I promise, I'll still be here after you wake up. I'm not going anywhere". The way her shoulders slumped I knew that I had won this time.

I hadn't realised that my movement had let the people outside the room know that I was awake, as they had stopped arguing and were looking at us, all wearing different expressions. I blushed and retracted my hand to my side as I prompted Jemma to go.

Natasha walked in, closing the door behind her giving Fury a look, and letting him know that he was not to come in. As she came to my side, she pressed a bottom at the edge of the bed and the window walls fogged up, making it impossible to see what was going on outside. Huh… how come that wasn't on before? I wondered, but my attention was diverted back to my sister as she sat on the chair next to me.

I noticed her tangled hair, her slightly dirty face and a gash on her chin. "What happened?" I asked, my hand lifting to touch the red spot, but I thought better of it and brought it back on my lap.

"Nothing I couldn't handle," she said with the voice that she reserved just for me. "I came as quickly as I could. How are you feeling?"

"I'm okay. Mostly tired. I think I have enough drugs in me that it wouldn't hurt even if I started running" I chuckled but then felt a pull on my stomach, followed by some pain. I gritted my teeth, hissing as I tried to resist putting my hand over the aching area. "No laughing got it". I opened my eyes, which I had shut tightly until the pain subsided, and smiled at Nat. "I'm good, nothing to worry about. Got all patched up. Plus, I doubt I'll be doing anything resembling any sort of physical activity anytime soon. Not if Jemma and Pepper have any saying in it".

"And me. And Clint, and May, and Bruce" Natasha added. "Even Stark, not that he would ever admit it to anyone. Well, maybe to Pepper. And he probably has J.A.R.V.I.S. on high alert as well".

I really wanted to pay attention to Natasha, but my powers were acting a bit weird because of the whole situation. And while I was not shaking anything, I couldn't exactly tone down feeling what was going on around me. And Fury was being very obnoxious. Pacing back and forth, feet hitting the floor hard that the vibrations were equally as hard. He might as well have been shouting this whole time.

I closed my eyes and rubbed them with my hand, feeling a headache starting to build. I must have grimaced cause the next thing I know, Natasha had stood back up and looked at me with even more concern than before. "What's wrong? Do I need to call Bruce?"

"No, I'm good. He's just very loudly restless for my powers" I sighed. "You said something about May before. God, I haven't even— has anyone called her yet?"

"Don't worry about it, she's been kept up to date through the whole situation and knows you'll call her when you can. Do you want to do that now?" She asked.

I shook my head. "I need to deal with them first. If he doesn't stop his pacing it will only get worse. I'll call her after. Do you mind giving us the room? I might as well get it over with"

She seemed reluctant like she wanted to argue. But she knew that once I made up my mind there was no changing it. "Want me to stay?"

"That's alright. I'm sure he already knows you will be staying right outside the room. I'll call you if I need anything. Plus, Maria will keep him in check, don't worry"

"I'll make sure she will," she said and made to move out.

"Love you" I called out before she got to the door and the most genuine smile spread on her face. "You too," she said before leaving.

I could tell that she was having words with them, as they took a while to get in here. This gave me some time to think about everything that led to me being on this bed and some decisions that I made that I knew Nick would not be very happy with.

And not long after I started contemplating things, the door opened and, quietly, the two of them walked in. I didn't even try to sit straighter, just inclined my head in greeting. "Maria, Nick. Hi. Despite them, and especially the latter, wanting to really talk to me, the concern was visible behind their eyes. "Please don't ask. I'm alright, just somewhat tired"

"Well, excuse us for caring," Fury said as he folded his hands over his chest. An annoyed expression on his face trying to mask his worry. It was weird. Sure, he had been trying hard after the whole 'Coulson' debacle, but he wasn't the kind of person that outward showed concern outwardly. He wouldn't be in the position he is if he did.

"Did you guys get Quinn?" I asked instead of dwelling on the 'caring' part. I knew he wouldn't like it if I did and I didn't have the energy for an argument. "What about the team?"

"He asked for further assistance in hunting him down. But we can't do that without bringing even more attention to our side project. At least more attention than we already have by going after him in the first place" Fury reasoned. And while I knew he was saying the truth, it didn't sting any less.

"And he just accepted that he had to drop this one?" We both knew who he was since it was only one person that we could have been talking about. And being in the Tower didn't really make it a secure enough place to talk about that without accidentally alerting the others. "There's no way that he gave up, you know him"

Fury sighed. "He didn't".

"But with the team losing two of their members, having Ward in leave because of what happened, he didn't have much of a choice" Maria supplied.

I closed my eyes and let my shoulders slump a bit. The whole situation weighing down on me. The others noticed, so they stopped and gave me a moment. "Look, I am tired" I started. "Tired of the secrets," I said as I opened my eyes and looked at them. "I need to tell the others about him, I cannot keep it from them any longer," I said.

I saw Fury's jaw clenched and so I continued. "It's been hard since the beginning, keeping this in. And having to lie about it to my family? I don't think I can do this anymore. They deserve to know, and it would make things so much easier. It's been, what? About 3 months since I joined the team? I'm sure you knew that sooner or later I would ask this of you" I paused to see if he would say anything. Which he didn't.

Instead, it was Maria who spoke. "She's right, sir" He turned to look at her, his one good eye opening as he tilted his head as if saying 'You too?'. She lifted her hands in a surrendering manner. "You can still say no if you want to, but I believe that at this point it is her choice on that matter. Don't forget that I was against this whole secret, to begin with".

I listened in slight shock. I was unaware of this, I had wrongly assumed that she followed his orders willingly. She saw my expression and she understood what was going on in my head. "It's alright," she said with a smile and a gentle expression on. "You had every right to be upset with me"

At this point, Fury had given up on trying to change my mind, especially now that he knew that Maria was backing my decision. "I need to clear more of my schedule now, thank you for that," he said grumpily. "You will have to take care of it," he said pointing at Maria. "As for you…" his finger travelled in my direction. "You know that they will still not be able to see him, right? Cause if they do, he'll ask how they know you. And that will bring a whole lot of confusion to the table"

I stared equally as hard back at him. "I'm not hiding from them that he doesn't remember me, Nick. I'll tell them the whole truth, all of it. We will then decide, all of us, if it's a good idea or not to see him or wait. This will not be up to you" I said with unwavering determination.

He didn't like that. He didn't like that one bit, but there was nothing he could do about it. "Fine" was the only thing he said, and even that was hard for him to say.

I nodded and then felt sunk more in the bed, as I ended up spending more energy than I intended with this discussion. "What's gonna happen to the team now?" I decided to change the topic to something lighter-hearted.

"Well… Ward's punishment was shortened and we're still looking at a member to fill in while Simmons is here. And she is to remain here with you until you've made a full recovery. We're currently going through options, our best being agent Barbara 'Bobbi' Morse. May scouted her and she also has a degree in Biology. I'll send you her file later" Maria was glad to provide the information.

"That's good, I'll look them over and tell you what I think. Thank you" I smiled at her.

"No problem" she smiled back.

"This doesn't have to mean we give up on Quinn" Fury added. "I mean, S.H.I.E.L.D. will give up on him, stop the search. We don't want more attention drawn to us. But I am sure Stark won't mind keeping an eye out. And Natasha pretty much threatened to go after him on her own". He saw that I liked that and I could swear I saw the edges of his mouth title upwards the slightest. "He tried to kill you. We take care of our own" he said with conviction.

He did try to kill me, didn't he? But not only that. I could feel my eyebrows furrow. "He didn't just try to kill me," I said thinking back to the interaction we had before he fired his gun. "He purposely led us there, so he could shot me. He said he had his orders. That the Clairvoyant says hi" I looked back up at them, realising something else. Remembering something very important. "He knew!" I exclaimed.

My eyes stopped looking at them, instead of travelling back and forth as I was trying to piece the information together, to try and find the connecting link.

"What did he know, Skye?" Fury said, his tone concerned from how I was reacting to the whole thing.

I turned my attention back at him. "He knew that I was Skye! He knew that Jane was a cover, he knew that I was a S.H.I.E.L.D. agent, he said the Clairvoyant told him. How did he know that Jane was a cover?"

"Do we know who this Clairvoyant is?" Maria asked, trying to help out.

I shook my head. "No, no idea. The only people who knew who Jane was is the team. We used the cover twice while on missions, one of them being with Quinn, as I explained" I looked at Fury as he nodded letting me know he remembered.

There was a long, silent, but tension-filled pause. "That means that someone from your team leaked information", Maria said what I was unwilling to admit. "There are only two people unaccounted for and agent Fitz also knows your secret" she pointed out.

"No, no. No way. There's absolutely no way that Fitz was the one. I wouldn't tell him classified information regarding our project, but I trust him enough to know that he's not the one".

"That's good enough for me," Fury said. "But that could only mean one thing…"

"Ward's a traitor".

AN.2: So, I hope you guys like it. It was one of my longest chapters, but it is both on the anniversary of the story and it is the 100th chapter so I tried to make it special. As I said in the beginning, thank you so much for the support. I will also post this story on AO3 starting from today.

As for the story, as I mentioned this is the last chapter of Book 2. A sneak peek at Book 3, it's called "HYDRA Uprising". Honestly, plot-wise, this was the furthest I had reached. I have a few things that I know what to happen, but it's pretty blank so far. If anyone has any ideas or suggestions I would love to hear them :) I always appreciate your feedback. If you're a guest and have Tumblr, you can always message me there, or in AO3.

I hope you're all doing okay. This is it from me now. I will plan the plot as much as I can for Book 3 and then start writing it. It might take a while but it will happen, I promise you that. Take care, everyone!