A/N: I'm not going to be saying too much about this story. You're going to have to read and figure out most of it for yourself. I will say this, there will only be a few characters from the Arrowverse, mostly just Barry, Cisco, Caitlin, and a certain speedster villain who will be replacing Hive.

I am altering some origin stories (mostly Barry and our speedster villain's really) and Simmons was never swallowed by the monolith in this timeline. Though, the monolith will have an effect on this story.

Also, this story purely takes place in the S.H.I.E.L.D. universe at season 3, so all our metahuman characters are going to be Inhumans and this takes place in late 2015 to early/mid 2016. None of the canon season 3 of AoS has occurred in this story, just so you all know. With all that said, let's get started.

One more thing: shoutout to the writer pokemon fan 98 for inspiring me with his/her/their story: Running With a SHIELD at Your Back. Let's begin.

Antarctica

1400 Hours (Antarctica Time)

Several inches of snow covered the ground as it hardened and turned into ice. Snow fell from the sky at a relatively normal pace and form, at least as normal as snow could fall in a place like Antarctica. It was relatively calm, the winds weren't too light but they weren't too fast either. The sun was covered and unseen by the layers of gray clouds which ruled the sky and reigned with snow. Near the top of a cliff, a man covered in heavy and warm clothing was dragging a large, thick, black bag. Inside the back, there were several fish, big and small, that he caught during his little ice-fishing adventure. The man was covered in black pants, black boots, a long sleeve gray t-shirt, and a large, thick, dark blue coat over it. The man also had snow goggles covering his eyes, a mask covering his lower face, and his hood on him. Not that he needed any of this extensive clothing, if he wanted, this man could have had everything done in mere seconds. However, he preferred doing it the normal way, as normal as he could at least.

The man stopped dragging his large bag as he set it beside him, he stood over the edge of the cliff. He looked down and saw what he was looking for on the ground: the cave that was made of ice. Then, the man pulled off his large hoodie before pulling his mask downward, revealing a brown-haired beard and mustache to have grown on his face. He then pulled off his goggles, fully revealing his face as the goggles hung off his neck. Had anyone been around the man, close enough to see his face, they would've probably recognized the face of twenty-eight year old Barry Allen. However, no one else was really around. After all, this was Antartica, the only other people who could've possibly been here would be scientists for research purposes or the Discovery and science channels. Barry had been careful to avoid them and to avoid being spotted by them. Hell, he had spent years just avoiding being spotted. As far as Barry could see, he was all alone on this isolated, cold continent and he was perfectly fine with that. He had isolated himself from the outside world for years.

Barry carried the bag of fish he had as he ran at super speed through a snow-covered path that led to the ground. He ran at super speed, arriving there in less than a few seconds as orange lightning trailed him until he stopped running. Barry then continued dragging his bag the same way he was before as he entered the cave. He held the bag of fish over his shoulder, the cave getting smaller and shorter the further Barry went in before he stopped at a spot. Barry stood in front of a wall of ice ten feet tall that sealed off any other possible entrance into the cave. He raised his hand and placed it on a specific, marked spot on the ice wall. Then, a device hidden and encased behind the ice released a blue holographic light that scanned Barry's hand and fingerprints. The device then beeped once in a positive manner as the ice split into two vertical halves. The halves of the ice wall began sliding in opposite directions, opening up the secret room that was behind the ice. Barry entered inside as the ice wall doors closed behind him. The room Barry was inside in was fairly large, in front of him, there was an ice roof that was transparent. The ice was as clear as glass, Barry had built it to allow sunlight. He couldn't afford a Vitamin D deficiency, especially with his speed and enhanced metabolism.

Throughout the room, there were several computers, monitors, some equipment and tech. There was also a cot lying on some soft snow. Nearby, there was a machine designed like a refrigerator capable of preserving food and water at room temperature. Next to it, there was a water filter that could clear water of any bacteria, making fresh water. Barry had built the machines by himself. Such feats were rather easy for a man who graduated Harvard at age sixteen with degrees in biochemistry and engineering. That was after entering Harvard at age thirteen. Barry placed the bag of dead fish he had caught from ice fishing before removing his coat, goggles, and mask. He tossed it all onto his cot as he looked around the area.

In a flash of orange lightning, which lasted for a couple seconds, Barry packed up and filed everything in an orderly manner. The cot was rolled up and neatly tucked away and the machines he built were stacked next to each other by size and height. The pack of dead fish Barry had caught were aligned, the bones were removed and they had been cooked thanks to the heat of the lightning. Barry leaned against the wall as he sighed. Everything was easier with super speed, though he had to be careful when using it considering that he emitted lightning whenever he used it, lightning that could've spread and hit other things or other people. Barry then looked down at the fish as an instant memory came to his mind: the memory of the day he had gotten his speed.

Six Months and Two Weeks Ago

Barry had just come back from another day of fishing, he had set the fish right in front of them after taking them out of the multivariable cooking machine he had built. He had designed and built the machine to be able to cook, preserve and maintain the temperature of certain foods and drinks, really just fish and water. Barry then took a bite from one of the two moderately large fish as he hummed with satisfaction at the taste. Suddenly, he choked as he felt something building up inside him. He felt sick, as if rocks were piling inside his body. Barry stumbled away as he struggled onto his feet, he choked and choked as a large, rock-like layer encased his body, trapping him inside as he was frozen in his position. A few moments later, the rocky layer burst as Barry emerged out of it, his body vibrating, orange lightning coursing through his body and the irises of his eyes. He instantly ran forward when suddenly, he found himself bursting through the speed of sound, crashing into an area of the ice wall. The crash caused Barry to fall to the ground as the lightning stopped coursing through him, his body's vibrating stopping as well.

Barry got onto his knees and elbows as a look of shock concealed his face.

"What the hell?" Barry sighed.

Present

Barry had gotten his speed just six months after he had arrived and isolated himself in Antarctica. It had been a few weeks since his 'one-year anniversary' in Antarctica. For the past few years, Barry had disappeared from civilization, traveling the world and learning to defend himself. He did everything he could to fight for and protect his hometown: Central City. The city his father, the famous billionaire, polymath, and doctor: Henry Allen, had died helping protect. Henry had made it his mission to stand for justice in the city. When he died, everything he stood for had died with him and Central City had become overrun with crime and corruption. It was a practical hell-hole and was officially one of the most dangerous and most crime-filled cities in the world. Barry had spent years learning to fight for and protect it. Now, with his skills, intelligence, and newfound abilities, he was ready more than ever. However, there was a certain reason that Barry was going back now, one that concerned the famous day in two days that Central City awaited.

Suddenly, Barry's thoughts were interrupted as one of the computers next to him beeped. Barry pulled the laptop close to him as he saw the radar on it. He huffed upon seeing what he had on the screen.

"About time," Barry whispered, a look of slight nervousness and determination on his face.

Two Hours Later

1600 Hours (Antarctica Time)

Barry was sitting in one of the seats of a first class-styled private jet. He looked out the window as he saw the clouds and looked down at the ocean. It had been a couple hours since he had boarded the plane of the person who had come to pick him up from Antarctica.

"I can't thank you enough for this," Barry said, turning his head to face the person sitting across from him. "I really appreciate you doing this, Dr. McGee."

Tina McGee smiled as she leaned back in her seat. "There's no need to thank me, Barry. You're like family and your father was a dear friend of mine, there's nothing I wouldn't do for his son."

"I appreciate that."

"How've you been? It's been twelve years since you disappeared, that makes you what? Twenty-eight now?"

Barry nodded.

McGee sighed. "Well… Time passes rather quickly, doesn't it? Though, I have to say, it is good to see you again, Barry."

"It's good to see you too, Dr. McGee." Barry replied.

"You know you are more than welcome to call me Tina."

"The CEO of Mercury Labs, who has more than eight PhDs deserves that kind of respect."

McGee chuckled. "You really have inherited your father's sense of respect. That's a good thing. Sometimes, when I look at you, I can see the same Henry Allen I went to school and grew up with."

"He talked about you a lot when I was kid," Barry said. "You two seemed really close."

"We were," McGee admitted. "I was heartbroken when I heard of his death. As much as you were, I can assure you."

Barry nodded as he looked down, his face forming in emptiness upon the memory of the day his father died.

"We've got quite a mess to clean up for your return," McGee stated. "Seeing as how, for one, you've been declared legally and officially dead."

Barry frowned. "Dead?"

"You've been gone for twelve years, Barry."

"Right."

"Your money, resources, and other assets have been secured to an offshore account. Once I give you access, which I will, you should be able to access them fairly easily."

"Dr. McGee," Barry said, looking back up to face her. "If it's alright with you, I'd rather not let anyone know about my return just yet."

"No need to worry, Barry," McGee assured. "The only people who know are me and the pilot. Though, I have to warn you, it'll only be a matter of time before Central City knows Barry Allen has returned."

"I know. And they'll know."

McGee sighed. "It'll be four in the afternoon, Central City time of course, by the time we land in the city. The day after that would be-"

"I know what it is. It's my father's birthday."

"There's a ceremony being arranged at Allen Industries HQ. Are you planning on attending?"

"I am," Barry confirmed. "But today, when I get back, there's something I have to do. I have to carry on with what my father was trying to do."

"Which is?" McGee asked.

"Protect Central City. From the crime, the corruption, the injustice. My father devoted his life and resources to protecting the city, and I'm going to do the same. Only this time, I have more to fight with."

"Barry, I understand your desire to carry on your father's legacy but he spent years trying to 'save' Central City. He made progress but not nearly enough to change it. There's only so much that a polymath and genius billionaire can do for a city drowned in corruption and crime."

"Dr. McGee, that's not what I meant," Barry said, looking out the window as McGee frowned in confusion.

"I'm afraid I don't understand."

Barry took a deep breath, rehearsing his words mentally before speaking. "I am going to fight for Central City. But not as this, not as the son of a billionaire or as Barry Allen. I have to do it as…something else, someone else. With my abilities, I can do that."

"You're one of the Inhumans," McGee realized.

"I am. But unlike the rest of them, I'm going to use my powers to do something. Besides, they're not the only thing I've got."

"Are you sure you want to do this, Barry? I'll keep your secret and support in any possible way I can but this is a rather dangerous path that you plan on going on."

"I know the dangers of this, Dr. McGee," Barry said. "I'm ready."

McGee sighed as she got up from her seat. "Well, in that case, do get some rest. We still have sixteen hours until we reach the airport."

The CEO left for one of the nearby bedrooms that was also built-in to the jet as Barry was left by himself. He continued looking at the window, admiring the scenery that was below him as he mentally prepared himself for the emotional pressure of returning to his hometown. He had been gone for twelve years, having run away from and left home at the young age of sixteen. Just a day after he had graduated from Harvard with his two degrees in biochemistry and engineering. Barry stared at the window, thinking in his head as the thought of a certain person from his childhood immediately came to his mind.

"I'm coming home, Cait." Barry whispered.

Sixteen Hours Later

Central City

1600 Hours (Central City Time)

The S.H.I.E.L.D. helicarrier levitated several thousands of feet in the air as its engines ran more powerful than ever. The carrier was capped to be roughly twenty thousand feet in the air. Thankfully, to the credit of all the technology, gadgets, and features on it, the helicarrier had its invisible cloaking features activated. This allowed them to be transparent to anything or anyone that tried or could have observed them. The cloaking device even allowed them to negate infrared and satellite tracking. It was one of many useful gadgets on the ship. Inside the carrier, S.H.I.E.L.D. agent Daisy Johnson stood next to Director Phil Coulson. The two of them were close as friends and teammates but they were able to maintain a professional, work-like relationship with each other in front of other agents and the rest of S.H.I.E.L.D. The pair of them were eyeing security footage of two new Inhumans they had managed to save.

"This is a big one," Daisy said, acknowledging their new victory.

"Two new Inhumans from Central City," Coulson stated. "We were able to get them both and we got to 'em before our new black ops group did."

Daisy sighed. "Along with Joey, these two are the only Inhumans we were able to get before them."

"You identify them?"

"Mack and I spoke to them, he's debriefing Joey and Yo-yo before they help out. They're shaken up and a little scared but they spoke to us and we've put them together. Thought it would be nice if they had someone to talk to the whole time. The guy is Cisco Ramon. Thirty years old, engineer, works at Mercury Labs. He gets fish oil about every month or so. Same case with the woman, twenty-seven years old. Her name's Caitlin Snow."

Coulson frowned with a look of realization. "Snow? Isn't that-"

"The family that raised Barry Allen after his father died?" Daisy asked. "Yeah. Same one."

"I know everything about it," Coulson said. "Barry Allen, last seen twelve years ago at age sixteen. He'd just graduated right out of Harvard with a degree in biochemistry and engineering."

"Talk about being a child prodigy."

"If that isn't enough, Allen entered Harvard at thirteen. He was able to change a car engine when he was six years old. Built an explosive out of base elements and chemicals when he was nine. For a science project, he made an electric-powered gas-free motorcycle when he was ten. He's been emotionally and socially distant ever since he was eight years old."

"That's when his father died," Daisy said as Coulson nodded. "What ever happened to his mother? I've always heard a lot about his father but there's almost no mention of his mother."

"Henry Allen claimed that Barry's mother died when Barry was extremely young," Coulson explained. "Even when she was alive, she kept a private life. Henry said she wanted to be out of the spotlight and live a private life. There's always been conspiracy theories and wild guesses as to who she is but no one really knows."

Daisy's face lit up with surprise. "So no one knows the wife of one of the smartest and richest men to ever walk the planet or the mother of his even better child?"

"Like I said, there've been theories and guesses. A common theory is that Tina McGee, the CEO of Mercury Labs, is Barry's secret mother and Henry's secret wife. The two of them did grow up together and were childhood friends. McGee denied the theory though and there's no confirmed identity of Barry's mother."

"It's sad Barry Allen has to go through that," Daisy acknowledged, remembering the childhood pain she had gone through. "No wonder he disappeared, even at sixteen. He probably just decided he had enough with the world and wanted to leave."

"A lot of people have been thinking he might come back," Coulson said. "All of Central City hopes he does. After Henry died, crime in the city spiked with insane rates, it was one of the biggest crime waves in U.S. History. Barry leaving only made things worse and now, the city's practically a living hellhole."

"All that just because Henry Allen died? Seems a little off."

"It's not just about Henry's death, it's about what he did. Henry did everything in his power to help Central City, to help it recover from poverty, crime, and whatnot. When he died, everything he stood for died right with him. The city needed a figure like him to rely on, a figure to follow. That's why they want Barry back, they need him to be that figure."

Daisy nodded her head, taking Coulson's words into account. "Barry might not be coming back, if he won't be this figure that Central City needs, maybe someone else will."

"Meaning?"

"I don't think the city needs Barry Allen," Daisy suggested. "It just needs a North Star to lead them and it's only a matter of time before someone else steps up."

Central City

1730 Hours

Dressed in dark clothes that negated the light coming from the evening, orange sun, Barry Allen rode his motorcycle through the streets of Central City. He had his black, motorcycle helmet on, allowing him to completely conceal his face. He didn't want all of Central City seeing or recognizing him just yet. Unknown to the city and its citizens, he had landed in the Central City airport over ninety minutes ago. Tina McGee had given him the motorcycle that he wanted to ride back on and the keys to a certain facility Barry would be using for a place to stay among other things. Barry drove his motorbike through the streets of Central City as he drove down the path towards a certain building that was in front of him.

Barry arrived at the S.T.A.R. Labs research facility headed in Central City. The company used to be a subsidiary of Wells Technologies, formerly headed by its CEO: Harrison Wells. It was then sold by Wells to Henry Allen, who wanted to invest more in the facility and use it better. After Henry died, the facility was closed off due to no one else having been able to step up and take ownership of the facility. When he had died, Tina McGee had assigned all of Henry's wealth, resources, money, and assets to an offshore and undisclosed account. She knew Barry wasn't ready to take on that kind of money or power but she didn't just want to erase Henry's legacy and let it fall in the hands of the federal government. As a result, she had sent it all to the offshore account, giving access to Barry when he felt he was ready and now, he was. In some ways.

The door to the gate that surrounded the entire S.T.A.R. Labs facility opened as Barry pulled the key out of the lock, sighing with somewhat relief that the key worked. Barry opened the gate, pulling his motorcycle inside before closing and locking the gate. He made his way into the labs as he opened the main door with relative ease as he entered the first floor. Barry took his motorcycle downstairs to the basement, moving it with his super speed as he parked it near the several cars that were parked there as well. Clearly they were Henry's. Barry and his father had grown up here ever since they had gotten this facility.

Barry then rushed with super speed to one of the higher floors as he entered the main cortex. Several childhood memories of Barry's childhood and his father rushed back to him as he stepped inside the area, hands in his pocket. Barry nodded his head, he knew what he had to do.

"Okay," Barry said. "Time to get started."

A/N: I will do a deeper dive into Barry's origin story throughout this book and other chapters. I'm not explaining any of the new origin stories for these characters through the author's notes. I'll explain and cover the, shall we say, complication surrounding Barry's mother in this story. Aside from the fact that the actress for her will be different than the one we had in the Arrowverse, I'm not giving away anything about her. If you're interested in what happens next, do leave a review and drop a follow and a favorite.