Chapter 1

Summary: Skye used to be a nobody. She had no family, no friends and no place to call home. She was the perfect target for Hydra. 7 years after being kidnapped by Hydra, she is becoming somebody, she has become Daisy Johnson, one of Hydra's best agents and secret weapon.

Note: Takes place during 2x03 where Jemma and Bobbi infiltrates Hydra.

This is also a draft.

Phil Coulson, the director of S.H.I.E.L.D, was sitting in his office, staring at the holographic screen that was displaying the news worldwide. Everyone was reporting on how S.H.I.E.L.D had become a corrupt organization after Hydra came out of the shadows and while Coulson never displayed any signs of resentment towards the news, he had to say that those reporters were starting to get on his nerves. They don't know what they're talking about, not all of S.H.I.E.L.D was compromised… okay that wasn't entirely true. Even his team was compromised by a hydra agent.

"S.H.I.E.L.D has fallen, Ward has betrayed us and managed to escape, Fitz has sustained a permandnet brain injury and Simmons has infiltrated Hydra's secret base to gather information" Coulson rambled on, voicing his thoughts out loud to no-one in particular.

May turned her head to look at Coulson with her infamous stoic expression which had been misinterpreted as her being bored 90% of the time, "Your point being?"

"Rebuilding S.H.I.E.L.D is going to be a bitch" Coulson stated bluntly causing May's stoic expression to crack for a few seconds as she smirked at Coulson's comment.

May grabbed the tablet that was displaying several portraits onto the screen, "Bobbi Morse is one of the best agents since Romanoff herself, she came second to Ward. Sending her as an undercover agent to protect Simmons while gaining information on Hydra's secret weapon was a good call"

Coulson leaned back into his chair, he still felt guilty for sending two agents to infiltrate hydra, especially when he had limited agents at his disposable who he could trust. When interrogating Ward, Ward had slipped up and mentioned a secret weapon that Hydra was able to control. Apparently, this secret weapon of theirs could bring down buildings and destroy cities in a matter of seconds.

"I sent 2 of my best agents into the belly of the beast" Coulson stated while staring at the head portrait of Bobbi and Jemma, "This doesn't feel like a good call"

"Have you spoken to Rogers? Thor? Maybe Stark? About all of this?" May knew that the situation as dire. She knew that if push comes to shove, the avengers would have their backs… well after they get over the fact that Coulson who was supposed to be dead was now alive.

"Speaking to them would mean revealing that I'm alive" Coulson muttered, revealing him not being dead to the avengers didn't seem appealing, especially when he knew how Romanoff and Clint would react, "And right now, I need to focus on rebuilding S.H.I.E.L.D as well ensuring that Agent Morse and Simmons make it out of Hydra alive"

Daisy Johnson was drumming her fingers along the wooden bar table that was disgustingly covered in something sticky. She waved down to the bartender, who happened to be her ex-boyfriend, to give her a drink.

"You're back alive", Miles stated with no hint of joy that made Daisy think that Miles couldn't give less than a shit about whether or not she died or not on that mission.

"Sorry to disappoint" Daisy replied sarcastically as she grabbed the beer out of Miles hand to drink. She turned her attention towards the tv that was hanging in the corner of the bar and was surprised to see that Hydra had revealed themselves, "What the hell did I miss?" she muttered to herself.

Miles followed her eyes and saw the news, "Yeah, Hydra was exposed a couple months ago"

"No shit" Daisy mumbled as she kept her eyes trained on the tv. How the hell did she miss this? She was only gone for a couple of months on a mission in Siberia. If she knew that Hydra was on it's way to become well-known to the world, then she never would have taken the job in Siberia, she would much rather stay here and watch things blow up, "What happened?"

"Apparently, that guy with the American shield released the redacted files about Hydra being Shield… or is it shield being hydra?" Miles asked himself with confusion.

"Either way Hydra is out in the open now" Daisy stated her thoughts out loud, "which means that the organisation is more vulnerable than ever… hey, what happened to the shield agents?"

"You mean the agents who aren't hydra?", Daisy nodded her head at Miles question, "There's a rumour going around that Nick Fury passed the job of being a director to someone else, either that's just a rumour, or someone is rebuilding shield in the shadows"

"Rebuilding shield?" Daisy scoffed at the idea of someone rebuilding shield when shield is technically Hydra, "If they manage to defeat Hydra, I might just give them a pat on the back"

Miles scrunched his face up in confusion, "Aren't you one of Hydra's best agents?"

"So?"

"I thought you'd be… I don't know, more loyal to Hydra. Hail Hydra, right?"

Daisy stopped herself from scoffing at the thought of her being loyal to hydra. Being loyal to someone sounded so… restricting. She hated the idea of having her freedom stripped away from her and being loyal to someone would be the same as giving up her freedom. She liked to think of herself as a personal assassin for Hydra, as long as they pay her well, she will play along with this Hydra act.

"Come on Miles, you and I both know that commitment is just not my thing"

Miles let out a rough chuckle, "Trust me, I learnt that the hard way"

Daisy was going to say something sarcastic but before she could, her private phone that was only reserved for Hydra operatives who had a high enough clearance level to know about her, went off. She looked down at the message on her phone that told her to go to the nearest Hydra. Daisy let out an annoyed huff, she had just gotten back from her mission, what the hell did they want from her now?

"Another mission so soon?" Miles asked as he took her empty glass.

"Unfortunately,"

Daisy reached into her wallet to pay for her drink but before she could pay for her drink, Miles shook his head and said, "It's on the house"

Daisy nodded her head as her way of saying thank you but just before Daisy could leave, Miles called out to her, "Hey! Stay safe alright? With all this shit going on between Hydra and Shield, you're bound to get dragged right into the middle of it"

Daisy knew what Miles was saying was true, "Careful Miles, you almost sound like you care" she responded sarcastically.

"Believe it or not I do care. Foster kids gotta stick together right?"

Daisy looked into Miles eyes to see whether there were any signs of manipulation or deception, but there was nothing of the sort, "Yeah"she mumbled before leaving the bar.

Jemma couldn't believe that this was part of her routine. Waking up at 5:45 a.m, imagine being chased by Hydra agents by running on a treadmill for a solid hour or so, and then prepare to leave for work in Hydra's base. She had to admit that it still felt a little odd for her to be carrying a cup of coffee into the laboratory that she had been working in for the past 3 months so casually. Herself from a year ago, wouldn't believe the position that she was in right now… well to be fair, a year ago she didn't know that Ward was going to betray them, and that Hydra was Shield all along.

Everything was still new to her and she had to admit that she was internally panicking 90% of the time. She was terrified that her identity would be exposed. It was difficult trying to focus on her job as a biochemist when she was constantly looking over her shoulder.

Well… to a degree, her fears were mitigated by the revelation that another agent had infiltrated Hydra with her. She knew that Bobbi was here for her own protection. It was reassuring to have someone as great as Bobbi by her side.

As Jemma made her way towards her desk in the laboratory, she noticed that there were a lot of agents lined up in the hallway. It wasn't unusual for agents to escort a prisoner through here however something was different, Bobbi was here, and Bobbi was almost never here.

If Bobbi was here, then something big was happening.

"Simmons, you're here early"

Jemma, who was slightly startled, turned around to look at her boss Kenneth, "Oh yes, I just wanted to get a head start on the new dr—"

"Save it for the report" Kenneth said, not wanting to hear the boring details of why Jemma was here so early in the morning.

"Right" Jemma muttered, feeling a little dejected at being dismissed like this. Just as Kenneth was going to leave, she quickly asked, "Do you know why there are so many guards in the hallway?"

"I don't have the clearance to know and neither do you" Kenneth once again dismissed her and walked away with his eyes glued onto the screen of his tablet.

"A simple no would suffice" Jemma mumbled under her breath as she watched Kenneth walk away. She pretended to be working on the new drug that she was studying. She was more focused on the guards lining up and Bobbi who didn't even spare her glance.

Bobbi was standing at the foot of the door with her hands behind her back, like a soldier would do when waiting for a superior office.

Oh! Maybe that's what they're doing, greeting a superior hydra agent. This was getting more and more interesting.

"Hail Hydra" The soldiers shouted as they saluted.

Jemma's eyes moved towards the figure who had just walked through the doors. She was expecting to see a buff man with a lot of muscles and a medal pass through those doors, but instead, she saw a young woman who was definitely in her 20's, with no chains or handcuffs around her wrist, which meant that she was most definitely not a prisoner.

"There's literally no reason for the salute"

Jemma's eyes widened in surprise, never had she heard someone speak so… informally. She looked over to Bobbi to see if she had an explanation for this, but she could tell that Bobbi was just as surprised as she was.

"I was ordered to escort you" Bobbi spoke for the first time to the young women. The young woman looked at Bobbi suspiciously and Jemma knew that if she was in Bobbi's position right now, she'd be sweating bullets.

"And you are?"

"Bobbi Morse" Bobbi answered, keeping her voice firm and steady. Jemma had to admit that she was kind of jealous of how composed Bobbi was, but in all fairness, Bobbi had undergone rigorous training to become the agent that she was today.

"Daisy Johnson" Daisy introduced herself. Jemma's mouth practically dropped when she heard Daisy introduced herself, it was such a minor act yet, it was out of the ordinary for a hydra agent to do so. Bobbi herself, had to admit she was shocked, never had she met a hydra agent who had resembled something even close to having manners, maybe it was because the girl was barely older than 20, but from her experience, young age is what made soldiers more ruthless, "You're new?"

"Yes ma'am" Bobbi internally cringed at calling someone younger than her 'ma'am', but she didn't know what to call this woman. She was obviously younger than her however, Bakshi had informed her that she had a higher clearance level than anyone in this building, which included her. So technically, Daisy was her superior. It was odd to think that someone so young could be her superior.

Bobbi looked up to see Jemma mouthing, 'Ma'am?' with judgement. She knew that Jemma wasn't going to let that one go.

"Ma'am?" Daisy usually wasn't bothered by the comment but something about this new agent seemed… off, not exactly in a bad way but not in a good way either, "I think we both can agree on the fact that calling me ma'am is awkward… just call me Daisy or Agent Johnson"

Okay, that was not what Bobbi was expecting, "Yes, Agent Johnson"

Bobbi began escorting Daisy down towards Bakshi's office, but she immediately stopped when Daisy coincidentally, stopped in front of Jemma's desk. Both Bobbi and Jemma held their breaths, fear was pumping through Jemma's veins as Daisy's eyes scanned Jemma while Bobbi's veins was pumping with adrenaline, ready to protect Jemma and fight off everyone in this facility if their identity was compromised.

"You're new to" Daisy pointed out. Jemma wasn't sure if she was afraid of the young girl herself or if she was afraid that her undercover was breached. Daisy looked at Jemma and then back at Bobbi before breaking out into a smile, "About time Hydra hired people who weren't so dull", Daisy looked around the other agents who all looked the same to her, "No offence… you know what I'm just going to go"

Just before leaving Daisy dropped her voice low just so Jemma could hear her, "Drop the smile and the fake enthusiasm, you don't exactly blend in"

Jemma's eyes evidently widened, oh god no, she has been compromised. She expected Daisy to say something out loud but instead the young women simply walked away.

"Shit" Jemma muttered under her breath. Did Daisy know that she was undercover? Was she going to tell Bakshi? Oh no… was Bobbi's cover compromised as well?

Bobbi didn't know what Daisy said to Jemma, but seeing how Jemma's eyes widened in panic, she was going to assume the worse and say that their covers has been compromised. Her fists remained clenched and her whole body went tense, if Daisy outed her to Bakshi, then everything will go to shit.

Bobbi opened the door for Daisy to enter, she prayed to god that she was being paranoid, and that Daisy didn't know anything. It was impossible right? There was no way that this random agent who she has never seen or heard of before, knows of her affiliation with Shield.

"Thanks" Okay… so Daisy wasn't a complete asshole. She had enough human decency to say please and thank you to others. To a degree, that was reassuring but at the same time it was unnerving to meet a hydra agent who seemed… so different to the rest of them.

"Bakshi" Daisy stood in front of Bakshi's desk with annoyance written on her face, it reminded Bobbi of a teenager who was annoyed at someone for interrupting their peace and quiet, "I literally just got back from Siberia, why am I being called into work?"

Bobbi has never heard an operative or hydra agent speak to Bakshi like this before and she had to admit that she liked the young girl's energy. Fuck, this undercover thing was going to become a lot more difficult if she grew to like the kid.

"We need you to accompany us on a mission. Remember Donnie Gill?"

Daisy cocked an eyebrow at the guy, "Seriously? I've been away for a long time Bakshi. I didn't even know that Hydra was exposed so why the hell should I care about some guy who has a weird cartoon name that reminds me of a fish"

Bobbi wasn't sure whether she should be amused by Daisy's comment about Donnie's name, or be surprised by the fact that Daisy didn't know that Hydra had been Captain America. She wondered what mission Daisy was on that would prevent her from being informed about the life-altering revelation… well, it was a life altering for her and her team at least.

"As you know, we began testing the new program"

Daisy clenched her jaw at the mention of the new program that Bakshi was talking about, if Bobbi didn't know any better, she would say that Daisy didn't like the idea of brainwashing someone, which was interesting to say in the least.

"Should you be talking about this in front of her?" Daisy questioned as she nodded her head towards Bobbi, "No offence" she said directly to Bobbi who wasn't fazed by it.

"None taken", Bobbi dismissed casually, if she was in Daisy's position then she would react the same way… especially if Daisy knew that she wasn't who she said she was.

"Agent Morse has a higher clearance level than half of the agents in this building plus, she has contributed to the program in more ways than you"

Daisy rolled her eyes at Bakshi, she never liked Bakshi, he always talked down to her as if she was a child… which she technically was in comparison to him, "I asked whether she can be trusted. I didn't need a whole TED talk on why she's an asset to Hydra"

Bobbi watched in fascination as Bakshi growled at Daisy's comment. Usually, this was the moment where Bakshi would order her to take Daisy to the rehabilitation room however, from where she was standing, it looked like Bakshi couldn't touch Daisy, and she wanted to know why Daisy was so important.

"Just…" Before Bakshi snapped, he took in a deep breath and finished off what he needed to say, "Donnie Gill has been compromised and needs to be taken in for rehabilitation. You must accompany us to Maribel del Mar to ensure that Donnie Gill is no longer a threat"

There it is, they wanted Daisy to go on the mission to eliminate Donnie Gill if things go south. Daisy knew that Hydra didn't care about Donnie, the only thing that they cared about was whether he was a threat or not, "Is this an order from you or Whitehall?" she questioned causing Bakshi to slam his hand against his desk and stand up.

"Quit being a little brat and do as your told" Bakshi scolded Daisy as if she was a kid but Daisy didn't even flinch.

"One day, I'm going to rip out your vocal cords. Your voice irritates me" Daisy replied with a sarcastic smile, she turned her head to look at Bobbi, "I don't know how you take commands from someone who sounds like a squawking eagle"

"Get out!" Bakshi screamed, veins were practically protruding out of the man's neck. Daisy gave him a fake smile before leaving the room. The second that she left Bakshi fell against his chair and rubbed his face tiredly, "Damn brat"

Bobbi thought that now was as good as a time as any to extract some information out of him. She walked over to his desk and asked, "I never seen her before, who was she?"

"A pain in the ass" Bakshi muttered as he looked at the files on his desk before tossing Morse a file with Daisy's name on it.

She picked up the file and immediately noticed how light the file was. There was only one sheet inside the file, she pulled it out and read it, "This is just giving her clearance to enter the base and go on the mission"

Bobbi scrunched her face in confusion and from what she could tell, Bakshi was equally confused although he was more annoyed than anything, "Precisely, there are no files or records on her"

"Isn't she an agent working for hydra?" Okay, this was getting weirder by the second, she needed to report back to Coulson and let him know about Daisy. D\

"Working for hydra?" Bakshi scoffed as if it was the stupidest idea in the whole world which only caused Bobbi to grow more confused, "The girl absolutely despises this organisation"

Okay, so if Daisy hated Hydra, why the hell did Whitehall bring her into Hydra's secret base?

"Then why the hell did you bring her into our secret base?" Bobbi shouted, acting as if she cared about the wellbeing of this organisation when in reality, she would personally love to see this place burn.

"Wasn't by choice" Bakshi retaliated defensively, "For whatever reason the girl has a high clearance. She's practically a shadow hidden in darkness"

Bobbi leaned back into her chair, taking in the lack of information that was given to her. Maybe, just maybe she could get Daisy to come with her to shield. It was a stupid and reckless suggestion, but Daisy was an absolute mystery who might information on the secret weapon and hydra.