Chapter 1

16years ago

Skye is 8years old she just returned from her yet another family, she didn't understand why no one wanted her. She was back at the orphanage sitting on her bed, the nuns kept telling her not to worry that she was special and some day she would have a family. Skye just nodded and said what they wanted to hear, but deep down she was done trying. No one will ever want her, and she accepted that. Laying down she heard her door open groaning she put her arm over her eyes, she didn't want to talk to the nuns she was done talking. She felt her bed dip and someone laid back with her, she looked over to see one of her best friends grinning at her, Clint.

"Well?" he asked, she just groaned again not answering.

"That bad, damn what did you do this time?" he laughed slightly, they have both been to at least 3 family always being sent back. They both knew it was better to laugh then feel pity, that's what held them together.

"Nothing just not a good fit I guess, you know the drill" she said still not looking at him, he slowly grabbed her hand and just held it and laid there with her. After a while she spoke up again,

"When do you leave?" she knew Clint was turning 18 in a week, and he wouldn't have a place here anymore, she wanted nothing more than to go with him. But she wouldn't burden him like that she knew she wouldn't be able to get work at only 8 and he would have to support her. She didn't want to lose her only friend though.

"On my birthday I will take off, maybe travel a little bit" he told her, he wanted her to come with him so he could look after her but she was still so young she could still get adopted. He looked at her to see tears in her eyes, she was trying to hold them in.

"Hey why do we go out and look at the stars" she nodded slowly as he lifted her off the bed hugging her close,

"You will always be my little sister, I will come back for you when you are older I promise. You will always be my Skye" he kissed her head.

"I will miss you so much" she said quietly. He protected her even since she was dropped off, ever since she was a baby he looked out for her. He would come back for her.

After that night Clint saw a sign for the circus, his future awaited.

Skye sat with a little candle in her bunk it was June 18th Clint's birthday, every year she lit a candle for him and hoped he was safe somewhere. It had been 16 years since he left her, yet she never gave up hope she would see him one day. It was midnight and the bus was quite she couldn't sleep just like all the other years, she went into the kitchen to get a glass of water when she noticed someone else was up also Coulson.

"What's up AC?" she said walking over and getting a water from the fridge. He looked up with bags under his eyes,

"Skye why are you up, you should be sleeping" he told her, Skye smiled because he always played father figure with her and she didn't mind.

"Couldn't sleep, and I am guessing you either?" she raised a brow looking at him starring at his mug.

"I can't get it out of my head, what they did" he said softly, Skye went and sat with him.

"You can't keep letting it get to you, you are alive we both are" she said softly

"I know but who is to say they didn't change just my memories but more?" he sighed again, he didn't want to burden Skye with this especially since she has recovered from Quinn's shooting. He needed to vent though, he needed to get it off his chest.

"AC, we will get through this together. Now we both should get to bed, I have to wake up early to train with the Robot and you need to get your beauty rest" she smiled at him picking up his mug and washing it off in the sink. They both went to bed, but neither slept.

About a week later Coulson got an unexpected visit from Fury,

"Coulson I see the plane is still in good shape, good thing too" Fury said sitting down in Coulson's office.

"Director what can I do for you?" Coulson had a bad feeling in his stomach something was wrong.

"I need a favor, a big one" he started, Coulson raised a brow waiting for him to continue.

"I need the girl to come with me for an undercover mission," Coulson began to speak but Fury held up his hand stopping him,

"I know you see her as a daughter, and I know she was hurt a month ago. I wouldn't have come to you if I had another choice, but I don't I need her. She isn't known in Shield and I believe in her skills." Fury let that skink into Coulson, but he still didn't want Skye off the bus and where he wouldn't be able to protect her,

"What's her undercover mission?" Coulson asked and Fury sighed

"You know I can't tell you that Phil, I wish I could but this is something big and I can't risk her cover to anyone but myself" Coulson clenched his fists,

"So you want to take Skye off this plane away from her only family, to put her on an undercover mission that no one will know except you? Are you out of your damn mind?" Coulson almost screamed,

"Coulson I didn't have to ask you, she is a shield agent know I could've just ordered her to. I am asking because I know what she means to you, to this team" Fury stated calmly

"How about we let her decide?" he said and Coulson nodded asking Skye to come up to his office.

"AC what's up?" Skye said briefly before looking at Fury confused before turning her attention back to Coulson.

"And who's the pirate?" She asked crossing her arms over her chest.

"Skye this is Director Fury, Director this is Skye" Skye's eyes suddenly went wide, why the hell was the Director here.

"Skye" she said holding out her hand for Fury, he gave her a once over and grinned shaking her hand,

"Pirate, or Director Fury is more appropriate" he told her, she mumbled sorry and he just grinned again, this girl reminded him a little of Romanoff.

"Skye the Director has a mission for you, but only if you agree to it no one will force you if you don't want" Coulson studied her watching as she looked between Fury and him.

"What would my mission be exactly?" She said crossing her arms again,

"You will be undercover, but I can't say why in front of Coulson. No one will know your cover except myself" Fury stated and she nodded slowly taking in the information,

"Coulson can I have a minute alone with the Director?" Skye said, this might be her chance to really do something in shield. To become a better agent.

"Of course but remember Skye this is entirely up to you" Coulson said one more time before leaving and shutting the door.

Skye turned to the Director who was watching her carefully, just like she was watching him.

"So what is the mission, just to be clear I am already accepting" she stated and Fury smiled a little,

"You will be going undercover in an organization called Hydra" he started, Skye was confused though.

"Hydra was defeated in World War 2, Captain America took out the head leader Red Skull" Skye looked at Fury whose face went grim.

"Unfortunately they are hidden within shield, we discovered they are hiding in the shadows. Hydra is embedded in shield deeply, up to the top. The reason why I need you to go undercover is because I need to know when they will strike what they plan, do you think you can do that?" Fury asked and Skye bit her lip processing all this information,

"How many people know about Hydra being inside shield?" Skye asked sitting down.

"No one but me, I had uncovered numerous information linking them to Hydra but I don't know their plan. I do know that they will strike soon within a couple weeks or months" Fury said looking at her,

"Okay I'll do it" Skye said this was her chance to protect other, to protect the family that always protected her. Fury stood up but Skye wasn't done,

"Director there is something you should know," she looked up to see him waiting for her to continue.

"I am a 0-8-4, I don't know if you knew or it anyone else does but I think you should just in case" she said shyly.

"I know and I don't care, you are still the best for this. Between you being new and your computer capability you will do great. I will let you tell Coulson and your team, but your official story is that you are coming to help me out with security. I know you don't like secrets but this has to be one if we are succeed" With that he left briefly talking to Coulson then going down to May.

"Are you sure about this?" Coulson asked worried, she just smiled.

"AC this is my chance, shield has protected me my whole life and now I will be able to do the same. I'll miss you guys but I will be back as soon as I can." She hugged him tightly before packing up her things, she was ready to do this. She walked up to FitzSimmons with a tearful goodbye, Ward was emotionless as always, but he had sadness in his eyes,

"Well don't get too emotional Robot" she saw him crack a small smile.

"I'm going to miss you Rookie, how long will you be gone?" he asked and she shrugged,

"Not sure how long Fury will need me" she answered honestly, she was surprised that Ward wrapped her in a hug, she smiled and leaned into him when she stepped back he gave her a small kiss on the cheek and she blushed.

"I'll miss you Robot, but you have my number if you need a shoulder to lean on, don't forget that." she said almost tearful, she was growing strong feeling for Ward and now she was being taken away, but maybe it was for the best. She was surprised again when May hugged her as well. Coulson told her to call when she could and she nodded not knowing if she could.

After saying goodbye to her team she hopped into the SUV Fury was driving she was ready.

Okay so I hope you guys like it so far, I will be posting as often as I can. Feedback is great. This is my first cross over so please let me know how I am doing. Thanks!