This is (another) idea I had based on the AOS comics, The Coulson Protocols though you don't need to be familiar with them to read this. Hope you enjoy!

The kettle boiled and she sighed, pouring the liquid into the mug when she heard it.

The noises.

The footsteps outside of her apartment.

Her breath caught in her throat.

But it was the voices outside that caused her to drop the mug, the ceramic shattering on the wooden floor.

She needed a way to escape, to get out of there before it was too late.

The door to her apartment was a major no. Not with the people outside it.

The air vents… too small.

The fire escape.

That could work.

Before she knew what she was even really doing, she pulled up the window, and swung one leg over the ledge, and then the other.

The night air was cold, and goose bumps crept up her arm. She shivered, then started to make her way down, the metal clanging underfoot.

Two floors down, she saw them.

A figure in the distance. She shook her head, annoyed but slightly impressed. They were clever, extremely clever.

The figure approached her, tall, blonde.

"We're not here to hurt you," she said, and all Jemma could do was try not to laugh. The gun raised and pointed at her begged to differ. "Please, come with us, we'll explain everything."

Jemma shook her head. "No, not again. I'm not going to be a prisoner, not again."

The blonde looked at her, as if trying to figure her out, trying to figure out what she was saying. "Who do you think we are?"

"Hydra, A.I.M., Roxxon, does it matter? You're all the same."

"We're not any of them. We're S.H.I.L.D. We can help you. We want to help you."

She shook her head again. "No. For the first time in ten years, I'm free. I'm not a prisoner, not any more. And I won't be. Not again"

The blonde gave her a look of pity, gave an apology and then Jemma's whole world went black.

"It's her."

"Are you sure?"

"Definitely, I wouldn't forget someone like her. Someone with powers like hers."

"But, Phil, it's been years since you…"

"It's her."

The answer seemed final, and Jemma felt her stomach tighten. She knew they were talking about her and she recognised one of the voices.

The male one.

The one they called Phil.

There was something about him.

Something that seemed familiar to her.

She opened her eyes, taking in her new surroundings, her new prison.

It was glass, a bed along one wall, a chair and desk along another.

It was larger than the others she had been in.

But it was still a prison.

"You're awake then?" a voice asked.

The blonde woman from earlier. She had a pair of handcuffs in her hand. A look of regret and pity was worn across her face.

Jemma was definitely a prison here, despite all that they were thinking.

She sighed, bored almost.

It wasn't the first time that she had been here, in this position.

And with her life, it probably won't be the last.

The man who sat in front of her was her was the one from earlier.

Phil.

He gave her a smile as if trying to show her that he was a friend, that he meant no harm to her.

And she was inclined to believe him.

But she still didn't trust him. She was reluctant to trust him, after all that she had suffered, after all that she had been through.

"Ms. Steranko," he greeted, trying to make her feel welcome. Trying to make her feel reassured. "Or should I say, Dr. Simmons?"

She sighed. "You know who I am?"

He nodded. "I believe that we spent some time together, a number of years ago now."

Jemma nodded. "Hydra. They still talked about you, you know. They dedicated… they named that information about you. The Coulson Protocols, but that's why I'm here, isn't it?"

Coulson nodded, shifting the papers to the side of the desk. "We need your help Jemma. I know what Hydra did to you, to get that information. What the information is. And I don't think I need to tell you how bad it would be if it was used."

A pause. He was wanting her to speak. "You don't."

He nodded in sombre agreement. "They haven't used it in the years they had it. We take that as good, but one of our agents has found that the drive is for sale now. And if it falls into the wrong hands…"

"You want me to get it?"

He nodded. "We've wanted you to work for us for years now Jemma. You are an extraordinary woman. Two doctorates. You could be useful to us."

"You want me to work for you?" Coulson nodded. "Then why the handcuffs?" She raised her hands, still cuffed together.

He gave a heavy sigh, then un-cuffed her. She rubbed her wrists, glad to be free. "It was a precaution. Protocols."

She raised an eyebrow, trying to decider his thoughts. "Why should I trust you?"

Coulson looked at her. He knew she would be apprehensive, after all that she had suffered, after all that she had experienced in the past. "You can read my mind, you know that I'm not lying. You also know that S.H.I.E.L.D. won't hurt you. You know that we help people like you, work with people like you."

She continued to stare at him, working him out. Then finally she spoke. "Will you promise me my safety?"

Coulson nodded. "You'll be safe here."

She was reluctant. She didn't want to do this at all, but there was too much at stake. And she was responsible for that, and if worse came to worse, she didn't want to think about that. "Then I'll help."

He extended his hand out. "Welcome to Level One."

There are a whole bunch of comic references, and there will be, in this fic as I do enjoy my comics. This is going to have 10 chapters, posted about once a week. Hope you enjoyed.