Hey readers! This is going to be my longest project ever! This will be a crossover between the Bayverse Transformers and the Marvel Cinematic Universe. This follow the movies in the correct years they were released. For example, Iron Man came out a year after the first Transformers. However, in saying that, there won't be direct involvement with the first individual films of each superhero, as I believe that they wouldn't have connections with the Transformers until Avengers 2012. And there will be some other Marvel films not included as well, such as Guardians of the Galaxy, Captain Marvel, Thor Dark World and Ragnarok etc.

But I do have plans on how I will weave the two universes together, as I personally have not found a Transformers and Marvel crossover that I liked. So this is a I'm going to do it my way sort of thing. As for how far into the MCU I will go, for me, that ended with Endgame. I am not a fan of the newer movies at this time, except for Spiderman No Way Home and Guardians of the Galaxy 3, and the Loki series. With that said, I do plan on involving Unicron in some way within Infinity War and Endgame, as I feel Unicron and Thanos would definitely ally with each other for their own means.

As for the main original character, she is a mutant due to a science experiment before Steve becomes Captain America. She can shape shift into a humanoid reptile, and she could also changed her own appearance, meaning she can disguise as anyone she wants. And because of the experiments, her life will be longer than a normal human. But there will be more detail on that.

Phew! That gets some of that out of the way. And yep, this series will include Optimus x OC, and Loki x OC. I don't know how many books this will be decided into, but I will at least assume six, possibly. As you all know I write long books, long chapters and I love what I do. Expect a slow burn in the relationships too.

Like my other series, Heart of the Prime, Sam and Mikaela will not be present. I just simply never liked their characters.

Rating for this story will be for the violence, mild language, mentions of gore and blood, talk of medical trauma and maltreatment, sexual harassment, sexual innuendo, smut and sex scenes. Please enjoy the series.

"HELP!"

That was the sound of a young man fleeing for his life through the streets of Seattle. He was carrying a mask and a bag in his hands, along with a handgun which was currently empty of bullets. Rain was pouring down and lightning barely lit his way between the two buildings of the city. The wind howled as the wind rushed around the man as he ran between the buildings. Water splashed up around his as his feet hit puddles along his path. He was clearly terrified.

"HELP! Somebody, help me!" He shrieks loudly again in a desperate attempt to get attention. "AAHHH!" He skids to a stop as something lands on top of a garbage bin front of him. He backs away in terror as the angry eyes glare at him and he glanced around before running to the right. "HELP ME!"

With the rain, thunder and wind, no one would hear the man's screams. He was desperately trying to reach a road so he could lose the being who was chasing him. He needed to, or he would be dead, and he knew it. He made another left and yelped as he tripped over a small, red cart and nearly completely face planted into the cement. He scrambled to his feet without thinking and continued running with his adrenaline keeping him going.

He jumped and stopped when a metal ladder fell in front of him, and glanced up, thinking someone was there. But there was no sign of anyone as far as he could tell. But he knew not to be grateful as he jumped over the ladder and continued running. He could see car lights in the distance, and a stone wall in his way. But there were garbage bags and boxes by the wall, which seemed to be the only way he was going to be able to jump over the wall.

However, as he was able to reach the way, he felt someone grab the back of his shirt and pulled him back with a firm yank, throwing him onto the ground. He groaned loudly as he felt a pang of pain shooting up and down his back as air was knocked out of his lungs. He coughed and looked up, gasping in fear and began to back away. His pursuer simply glared at him as his pathetic attempts to escape were amusing to her. But she was already bored.

Stepping forward, she stamped on his chest and made the man cry out again, grabbing at her leg to try and pull it off, feeling soft scales underneath his hands. "If you think that anyone would want to help a rapist, murderer and thief, you are sadly mistaken." Leaning down with her glowing, green eyes, she stared in the man's brown eyes. "I would have ignored you if you were none of those things. But the world does not scum like you. And this…" She grabbed his bag and yanked it from his hand, and she heard the sound of jewellery within the bag. "All of this does not belong to you. It belongs to the store you took it from."

"P-Please…" The man began to plead. He had a hard time making out the shape of this being. He had first thought she was girl, but she was not. Her whole body was covered in scales, and she wore a thin, black dress to cover her humanoid body. Her tail was long, thin and had a sharp tip at the very end. "I-I…I h-have no choice…m-m-my…"

"If you are going to tell me that you had no choice because you need money for your family, I have heard it all before!" The creature grabbed him by the shirt and pressed him against a nearly wall harshly, making the man cry out again from the pain in his back. "I have no patience for criminals like you. And I am doing everyone a favor by not letting the prisons get crowded anymore than they have to. After what I witnessed tonight, you more than deserve death."

"P-Please, h-have mercy!" The man begged as he tried kicking at her stomach, which did not bother the creature at all and he tried punching at her arms instead, which again were not hurting her. "W-What th-the hell are you?!"

She simply grinned at him. "Let's just say, the nineteen thirties presented some very unique mutations for a lot of people. But you will never know them! Because you are nothing more than a monster."

"You're the monster!" The man snapped back and spat in the creature's face.

She hissed suddenly, making the man realize that was a mistake. She grabbed his neck tightly, making him gasp and cough as he grabbed her arm before she brought her left hand back and stabs her long, sharp claws into his chest, breaking his ribs and slicing the man's heart in half. The man's body trembled from the stabbing, but he went limp once the heart was slice, and the creature felt the warmth of blood pooling out of his chest.

Dropping the man's body, the creature allowed the rain to wash the blood from her hands as she stepped back, looking at his corpse with a shake of her head. "What a pathetic little man…they are all the same." She shrugged a little as she spoke to herself. "Just another criminal taken out…"

"And you must seem to think you are doing this country good by taking out one, little criminal." Jumping, the creature turned around in surprise and saw a man dressed in black holding an umbrella with an eyepatch over his left eye. He was bold and had a confident posture as he stared at her. "I apologize for startling you. I just could not help but notice your little mission just now."

The creature did not know if she should be weary of this man or not. But she couldn't see if there was anyone with him, so she relaxed slightly. "Who are you? And how did you even notice me? People never see me."

"I think you might be surprised, but we have been watching your movements for the last year. My name is Nicholas Fury, but you can call me Nick or Fury for short, whichever you prefer." She frowned a little as she listened to the man quietly. "I am with the government…" The creature widened her eyes and hissed, raising her hands with her claws ready. The man raised his hand to show he was not a threat. "Easy there, Saphira…" She blinked as he addressed her. "I know who you are. You are right about the mutations in the thirties. You were one of fifty, if I am not mistaken, to willingly undergo mutations to your body. And from what I understand, they succeeded. But they were going to exploit you, and you killed the scientists. Is that correct?"

She did not know how he got that information, and the fact he was working with the government was a bad sign to her. "So you somehow got their files. I thought nobody would ever find it. It was a bunker underground."

"I am afraid things like that aren't as difficult to hide as you might think, Saphira. But I want you to know I mean you know harm. I am with the government, sure, but I work for a special division in the government after I had encountered a very unique person a couple years ago." She was still suspicious of the man as she did not relax her defensive stance. "To be fair, the bunker was discovered by accident a year and a half ago after uncovering old files from the forties regarding it. It seemed that someone in the military at the time knew of the bunker and kept the file at the time."

Saphira relaxed a little as that made more sense. "So you thought you were going to find something else." Fury nodded affirmatively. "That means from the files, you figured out who I was after deciding to see if I was around…but those files would have told you my life expectancy is now much longer than an average human."

"That would be correct. And from what I understand, this form you are in is not the only thing you can do, am I right?" Saphira looked down at her body briefly before looking back at him with a frown. "You can breath fire and ice, can you not?"

"And lightning, yes. But…" Saphira stepped closer while still keeping a threatening composure. "I can also shape shift my appearance. I mean, I could easily take on your appearance, and your voice. And with a little glance inside your head, I can mimic anyone I want. I could take your job right now, and see exactly for myself what your special division is all about."

Fury did not flinch as Saphira stepped closer. He could see her scales glimmering in the faint light from nearby apartments. They were dark in color, but he knew she could change their color at will. "I want you to know that I am not here to tell you we want to experiment on you, Saphira. I want you to become part of something much bigger." She stopped and raised an eyebrow at him confusion. "All I will say there are just some things that are happening in the universe is bigger than I once believed. I had someone help me see that. But now we need extraordinary people like yourself to help."

Extraordinary people like me?

Saphira relaxed her muscles immediately as she was suddenly curious to know more about what he was trying to tell her. But she was still alert in case something was to happen. She wanted to be ready, so she would not be too stupid about it. "You have my full attention now, Fury." She stepped closer so he could see her better. "Are you trying to tell me that you met someone who isn't from Earth?"

"You can say that." Nick could see Saphira's appearance now. He was aware she could change her body to a reptile-like creature. She had a slightly longer neck than a human with a long snout full of sharp teeth. The snout shape looked similar to that of a crocodile, but it was off because of the mutation. The color of her scales were a dark blue, and her long claws were black. Her feet also had long claws, but she also had a raptor toe and the back of her ankles and legs had sharp spikes, making her feet extra dangerous. With her thin dress on her could not see anything else, but he didn't need to. And her tail was very long, and the long, sharp tip could easily impale anyone. "And it has made me aware that this world is completely unprepared for a threat that can come from behind the sky."

"I can believe that actually." Saphira was still completely unsure if she should fully trust this man, but he had an extremely calm demeanour about him, and he did not seem to be lying about what he was saying. "So what exactly do you want me to do?"

"There are just some things that we require your help with. Not only can you help by changing your appearance and sneak into places a normal person can't, your intelligence is also something we are interested in. I understand the mutations helped with that."

Saphira snickered with a roll of her eyes. "I might be good with numbers and science, but that doesn't make me smart, Fury. Are you going to tell me you need me to create an equation for weapons or something?"

"That won't be necessary. My part of the government is supplied by the Stark Industries, so weapons is not something we need." She recognized the name, but she said nothing. Fury reached into his pocket and pulled out a laminated picture of some kind of symbols. "These symbols here have been found around the world. We have reason to believe this is not Earth symbols."

Saphira looked at the pictures curiously as she did not recognize the symbols. But they were unique, and they were found in different history places. "I don't recognize these either. I never saw these in the last sixty years of my life. I am not really sure why you think I can help."

"I wasn't expecting you to know right away. But it is something we need someone to learn what they mean. I fear these symbols could reveal to us something that I fear is coming, and we need to know. And while I know you are smart with maths and science, I believe language is another strong element of yours." Saphira still did not know if she trusted this man or not, but she was still curious. "If there is more evidence regarding these symbols, we need someone one job focusing on them. But don't expect to be keeping your nose to the books all the time. Your abilities will mean you could be on the field too. And simple criminals like that man…" Fury gestured to the body behind Saphira, making glance back slightly. "Look like pieces of cake. And believe me, there are people out there who deserve this just as much, if not, more than that guy."

Saphira looked at the images with a raised eyebrow before she looked at his brown eye curiously. "And what would I benefit from this exactly? It seems to me you're interested in using me. Sure I could help, but I don't want to waste my time."

"You will be given protection. The government is aware of your presence, Saphira, and if you do not agree, there is a plan to terminate your life." She did not seem surprised by the revelation either, but Fury continued to talk. "Not only will you be given protection, but you will be given a salary, a place to live and you will not be treated differently. I can promise you that we don't want to use you, Saphira. I want you to stop living in the shadows. You don't have much of a life, other than going around killing petty thieves."

"He wasn't just a petty thief."

"You know what I mean." Saphira grumbled a little and kicked at the water below her feet. "I know this is a lot. But I really cannot leave without you. If I do, there will be no other chances for you." She softened her expression to a slight frown. She didn't like that at all. "The organization I have built is called SHIELD. It stands for Strategic Homeland Intervention, Enforcement and Logistics Division."

She hummed in slight amusement upon hearing what the name stood for. "I see…that doesn't sound anything like a planetary defence division of the government."

"We don't need to be too obvious. But I hope you are considering on coming with me, Saphira." She shrugged and looked away from him as she still didn't know how to answer him. "The fact you are cautious means you have a good head upon your shoulders. I would be more disappointed in you if you trusted me straight away."

"You would?"

"Of course. Why would I expect someone like you to just trust me like I was somehow your best friend?" He had a point. Saphira could not help but smile at him in amusement and decided that he really wasn't bad at all. In fact, this was probably the only chance she had. "But I do need you to trust me a little bit. I can work on the rest."

Saphira's smile widened and Nick would see her change suddenly. Her scales would fade away, replacing the shiny scales with pale skin. Her claws sunk into her nails and flesh, leaving no mark or clue that there was something very different about her. Neck shortened to normal human length, and her face flatten as her snout disappeared, returning to a normal nose and mouth. Her green eyes softened and her tail seemed to slither inside her tail bone. It was strange for Nick to see, but seeing her natural appearance was nice. Saphira is of Korean descent, and now that she was no longer feeling threatened, she could relax and show what she really looked like.

"It seems you are a man with strong words. I will soon see if you stick with it." Nick smiled politely at the girl and she stepped closer to him. "But I hope you do understand, Nicholas Fury, that if you are lying to me…you will end up in a worse state than the man on the ground behind me. And I won't make it quick and simple. I hope you know that."

"I am fully aware of that fate. However, I am very confident that will not happen." He turned to the side slightly and gestured for her to go ahead of him. "Ladies first."

She folds her arms with a shake of her head. "No…I don't know where you want me to go, Fury. It would be better if you lead the way. At least if there is a shooting squad around the corner, I can hope that they will shoot first, ask questions later."

The man chuckled as he understood that the girl was still assessing the situation, and he admired her carefulness. He couldn't blame her for it at all. He turned and walked away, and he heard Saphira follow him. Nick was glad that she did follow. He considered offering his umbrella to her, but as she was soaking wet, she likely would not want it. Plus, she may also refuse it for believing it could be a trap too, so he would make sure to be cautious about it.

Saphira kept a few feet behind the man in case he would do something. She had very fast reflexes, but that didn't mean much if he was thinking ahead of her. However, as he lead her through the alleyways, there was no firing squad. She saw no one else who could be suspicious at all. So far, everything seemed to be fine. But Saphira was no fool. Especially as he was leading her to a side street, and she knew that it was another place that could be dangerous.

However, Fury walked over to a black Mercedes e320 and opened the passenger door. There was no one in the car and the man looked her with a polite smile. "I believe this is your right, young lady. We have about a twenty-minute drive from here, and you can keep asking me a whole bunch of questions."

"I hope those twenty minutes don't turn into something we both regret." Saphira stepped into the vehicle and Fury did not respond to her cold response. He closed the door for her and ran around to the driver seat as Saphira put on the seatbelt. She looked at the man as he sat down and placed the umbrella in the backseat after shaking the water off outside. "Am I to imagine we are going to base?"

"Nope, the airport." Airport? She frowned as she had no passport or ID. "I have everything covered for you, Saphira." He gestured to the glove box and she looked at it curiously. "All of your important documents are in there. The government has had to do some fancy work to make sure they don't look suspicious against your old ID. What is your last name exactly?"

"Fernsby."

"That is definitely not a common name, and it will easily be picked up. I hope you don't mind, but we changed it to Verlice. That way it won't connect to your original surname."

Saphira Verlice…I don't mind it actually.

"But you do need ID to get on a plane, so that is why we had to do it." Fury drove away from where the car was parked and Saphira was able to relax a little more as nothing happened while they were sat in the car. "Your surname will probably get changed around a few times, so expect that. And maybe your first name, but only if you would be fine with that."

"No, I like my first name. But if you did change it, Sapphire would be the name I would want. It is very similar after all. Still…" She glanced out the window, watching the water from the rain run down the glass. "Where are we going? Are we going to stay in America? Or is this going to be a base outside of America?"

"We are heading to New York." New York city? "It is where I base a lot of my main operations. We won't be stuck there all the time, but it is a busy place. There are people I will introduce you too, and you'll have to meet with some government people."

"I do?" Saphira did not like the sound of that at all. "I am…well…at least if you are telling me that I have to shake hands with a senator, then I guess I am definitely not going to be shot on the spot…hopefully. Because heads will roll otherwise."

"I keep forgetting your flesh is thicker. But you aren't invincible, Saphira. Being stronger, more intelligent and able to change your appearance doesn't make you indestructible. That would be your downfall if you have a heap of that confidence. I am sure you know that." Saphira appreciated the advice, and she smiled as she was glad that he understood. "But I am not saying that because something would happen, of course. They want to meet with you because it's standard procedure. And they can relax. They've been on my ass about getting rid of you until I proposed this idea."

That meant Fury was advocating for her before he met her. That's never happened before in her life. If that was true, then this man was being truthful. "You…you didn't want me to die?"

"Absolutely not. I think it would be a complete waste of your life. After all, you were almost made a puppet after the successful mutations. I think it is best that they get put to what they meant to be for. For good." Nick glanced at her with a confident smile, and she felt herself trusting him a little more. "You were the only one who was mutated successfully, from what I understand."

"There were others. But…I actually don't know what happened to them. I saw them before I went in…" Saphira frowned as she thought about it before widening her eyes. "Were they in the cylinders when you went there?"

"I am afraid so…but…they were worse, and autopsies revealed they had been electrocuted to death, not drowned. Which meant those scientists killed the others when you came out." She felt a sense of anger upon hearing the fate of the others. They had been her friends, and she never thought to look for them, and she felt guilty about it. "I am sorry for the bad news. But I am not even sure if they would have been as strong as you to go against the scientists. You did a good thing."

Even though my friends were probably killed when I got out…I should have still checked.

But she now had a chance to show that her mutations can be used for good. If she really can put her abilities to better use than being a vigilante in the neighbourhoods and killing criminals that she sees, then it would be worth it. Saphira didn't really know if she could fully trust Fury just yet, but there was something about him that made her believe that he was not a threat. Sure, she was still on edge, but she wasn't weary of him. Plus, he already had a task for her. Learn what those strange symbols are, and potentially stop worse people that the criminals she was already killing.

"Well…I guess as the only who made it out alive…I will be doing this for them as well."

"And you will make them proud."

She smiled a little before looking out the window and moved her hands to her arms, feeling a little cool due to the water droplets on her skin and soaked dress. She still couldn't believe that she had gotten into Nick Fury's car, and was potentially on her way to New York city to begin a new life. Saphira had no idea if what she had done was even a good idea or not. But she really had nothing but her life to lose. So she was going to see if she was going to regret getting into Nick Fury's car or not.

And all this happened nine years ago. Life has never been the same for Saphira since 1998.