IMPORTANT AUTHORS NOTE - 02/05/2017

For all of you wondering - NO - I have not abandoned this story, but I had put it on the back burner until recently, when I finally decided to sit down, and flesh out where I wanted it to go.

I then began a major overhaul of everything I have written for it, both posted and non-posted, which has taken me quite some time, and is still ongoing as of this posting.

Chapters one through four though are one hundred percent ready, and chapters six and seven and roughly eighty percent complete - chapter five still needs some work though.

I have completely removed Ward's connection to the Queen family, as that was just a way of making him fill Oliver's shoes, and follow the original storyline which, 1). I didn't like, and 2). I received a lot of complaints about anyway, so I decided to remove Thea and Moira as factors. They still exist, and may crop up later on, but there will be no biological relationship there. The only cross-universe one is the one between Grant and Tommy, and I intend for it to stay that way.

A major intent for me now is to write an original storyline that ties in with AoS at some stage, as well as stays somewhat (read: extremely vaguely) connected to the CW's Arrowverse, which includes a flashback/young Ward storyline that borrows elements from Arrow, but is for the most part, completely different. As this is an Arrow AU, there will be some taking from the show, which non-viewers won't even notice, but I do hope that viewers won't mind, especially as I have tried to make at least a few changes, and these will become fewer and fewer as we go on.

We will also see a larger role given to supporting characters and their backstories, which is something I always find to be underdone on TV, as well as introducing other Marvel and DC/Green Arrow related characters in the pages to come.

Please enjoy, and if you would be kind enough, leave me a review in the comments box below.

-MarvelMatt

Chapter One: Prologue to the New War

"My name is Grant Ward, and for fifteen years, I worked as a traitor, before I was eventually caught. I had fought my way back to working SHIELD, away and against the death and destruction that calls itself HYDRA, as a way to atone for my sins, but like everything does, things changed, and I left to find myself.

I want to be more than just a weapon.

I want to be someone else.

I want to be something else"

Previously on Shadows of the Soul

Pulling over to read the signs, he smiled to himself. If he wanted to start somewhere new, he needed a city. One that he could learn the truth about HYDRA and S.H.I.E.L.D. in, but it had to be one he'd been to before, even if it was just to set up a temporary safe house with John. He'd still mapped out the city in his head.

Besides, if nothing else, this one had all of his own training gear stored away, under that abandoned steel factory. John had named the place The Foundry. For him, it was about to become HQ.

Re-adjusting his sunglasses, Grant Ward revved the engine, before kicking off, passing the highway welcoming sign that would lead to his future.

'WELCOME TO STARLING CITY'

Getting himself set up in a new city was the easy part. Thanks to one last favour from Fury, and then one fake classified data leak. His real identity was usable again, which meant that he didn't have to create another new alias, not that anyone had remembered his name five minutes after his brother's attempt at what was supposed to be a public execution announcement. A few people had sent him questioning looks when he'd had to give his name in, but no one had bothered to take too much notice of him. They probably all just saw it as a funny coincidence.

Small miracles, he supposed.

He'd taken a job at the Merlyn Global Group, working as a member of his daytime security staff for their highly classified projects. His SHIELD background, though it listed him as a high level hostage negotiator, had apparently impressed the higher ups enough to give him a starting position in classified, whereas most of their other employees had to work there for over five years before they were even considered for that division, and so now he started at six thirty every morning and finished at five every night.

He'd taken a rather large apartment in The Glades - the pay for years of working black ops that he had never spent meant that money was no real object to him, especially since he now had a similar wage again.

The Glades was definitely the seedier part of the town, with a well-earned reputation for gang violence and massive drug use. Most of the city's muggings, murders and assaults happened in The Glades.

They say violence breeds violence.

If he wanted to save this city, and then work on saving what was left of his own soul, then he had to know his terrain. A few days spent there fifteen years ago just wasn't enough. No - he was certain that the best way for him to do that, was to live within it. He had to breathe the city in every day, he had to know it intrinsically, as though the place was simply an extension of himself.

Like a tiger in a forest, he had to memorise his hunting grounds well enough, so that he could flow through it, able to give chase to his prey without thinking about the route he was taking.

His apartment was made up of bright canary yellow walls (not a colour he was a fan of), a dark wood floor and soft black curtains, with some sparse furniture and furnishings about - which were all in dark wood and black leather. A lone picture of himself, Triplett and Garrett, and the former's Academy graduation day was hung on the wall.

He straightened up as he exited his apartment, his black security gear helped him to blend in with the morning darkness, and squinting, he could make out the faint glow of the rising sun on the horizon.

Pulling his black leather motorcycle jacket on to help fight the chill of the October morning air, he pulled his motorcycle keys out of his jacket's front pocket, before he grabbed the helmet off of the countertop, and let the door lock behind him.

Pulling into Merlyn Global's underground parking area, he flashed his ID card at the gate, before sliding into a parking space, and cutting the ignition on his bike, before he slipped his helmet off and tucked it under his arm.

Passing by Mr Caine, the parking area's daytime guard and sending him a quick "Morning", Grant headed straight for the elevator and inserted his personal security fob, before pressing the button for the eighteenth floor, where he could store his gear, and get the day's assignments.

The elevator ride was as normal as it could be, the irritating elevator music droning on, almost in an attempt to lull him back to sleep. Not that it could of course, his training would never allow for it.

His training.

That's an idea that takes him back, dragging up his memories of the five years he spent 'training' in the trees, with the occasional bout of 'fun' with John. There was that whole mission he went on, pre-SHIELD to help John with-

Don't think about that!

He chides himself, he's always doing this to himself he thinks. It starts by letting his thoughts reach that, and then he thinks about John, then Coulson, and then he finally reaches Skye.

He thought he had loved her, but then he'd stabbed her in the back, and in the heart, on the words of a madman, and truthfully, he'd cared more about the madman.

They say that 'distance makes the heart grow fonder', but his feelings didn't feel any different to him.

So just what did that mean?

Is he in love with her?

Was he in love with her?

Did he even care for her at all?

Was she just a passing fancy because they lived in close quarters?

Was he still just angry at the way she and Hunter had treated Bobbi?

In fact, out of all of that, the only thing he was certain about was that he missed having Bobbi about all of the time.

It's been two months now since he left SHIELD behind him, but that particular train of thought just hadn't changed at all. Being around Bobbi was easy for him, she made everything seem just a bit simpler, and just more bearable, though he's glad he decided it was time he left.

Now he knows more about himself than he had before, more than just being the person John Garrett wanted him to be.

The weapon he wanted him to be.

He likes dogs, as well as his reading. There's no particular genre he prefers, though he has a tendency to pick up some of the more fantasy/mythology orientated ones. His music taste is unrecognisable to anyone that knew the old him. He used to listen to classic old-timey soft tunes that John preferred, whereas now, you could only find classic rock anywhere near his radio and CD player.

He still hasn't mastered the digital download yet.

Stepping off the elevator at his floor, he nodded a greeting at Eddie, who was just getting off the night shift, before stepping into the small office room their supervisor usually used, and took a quick look at the rota for the day. He was on the rounds all morning, before he had to escort a Doctor Thompkins, along with his or her classified material, to a meeting near the end of the day. After that he was off the clock, and today was the day he wanted to head down to 'The Foundry' - one of Garrett's old safe houses - and check on his gear and equipment.

It was almost time to go hunting.

"How's she doing?"

Coulson's voice cut through the stoic silence that May had immersed herself in, as he strode towards her, drawing to a stop when he reached level with her.

"Same as usual"

They both looked down from the viewing platform, watching as Bobbi took Skye and Simmons through some of the more basic training and breathing exercises. Skye had elected to restart her combat training under Bobbi, whose style was a bit smoother than May's usual method of trying and overpowering her opponents, while Simmons just wanted to learn some basic self-defence moves, just in case. Fitz had started taking a few similar lessons with Hunter, while Tripp generally offered advice and tips from the side-lines, where he was sat in his wheelchair.

The former weapons specialist had taken to the chair with a quip and a smile on his face, but May had occasionally caught him brooding, his depression over the situation setting in, marring his normally joyful features but then he'd go for his medical check-up, and they'd tell him that he had a very good chance of regaining full use of his leg, depending on how his physical therapy went.

But not a guarantee.

No matter how much she tried to justify it. No matter how much she told herself that he had been murdered, revived and brainwashed into doing Whitehall's bidding, she just couldn't quell the rage she felt towards their former specialist for what he'd done to Triplett.

Or maybe, she confessed to herself when she was alone, you just don't want to.

When they'd decided to put Ward back into the field as a black-ops specialist, operating without any back up, she'd been waiting for the call that he'd died on mission. Half-expecting and half-hoping that he'd get shot or stabbed, or even blown up, without any backup to call in.

And then she watched the video.

The video they'd taken in secret, expecting him to use the vacation days he'd been given to report back to HYDRA, before he'd asked for Garrett's ashes, claiming he wanted to bury him. Garrett had no living family, well, unless you counted Ward, so Coulson had eventually relented and given him three days off to sort it out.

Then Ward had left them for a few days, and made his way to some woods in Wyoming. They hadn't figured out why those woods were so important to him, but Ward had navigated them with a precision, buried his urn there, along with a dog bone for his old pet, but that wasn't what was important to them.

What was important to them, was the confession that Ward had unknowingly delivered them that day, and a small - very small - piece of her died, simply because of her treatment of him.

He wasn't just a mass murderer and a traitor, though he was those things, he was at his core, a lost little boy, one who had been manipulated and physically and mentally abused by a man, who he believed had 'saved' him from his own personal hell.

He'd saved him from his own hell, before he'd dragged him into a fresh one. It honestly made her pity him. To never know any form of love until he was twenty-six… it was no wonder people thought he was anti-social.

He really hadn't been hugged enough as a child.

And unfairly, she wasn't above admitting, she hated him for it.

A shrill squeal of laughter brought May out of her musings as Simmons had managed to sweep Skye's legs from under her, sending her crashing to the floor, much to Bobbi and Coulson's apparent amusement, as well as Skye's great disappointment.

She had been much more closed off since Ward had left for what was the third, and seemingly final time.

When he had 'died', and Arsenal had taken his place, she seemed as though a piece of her was lost along with him. She had been glad after he was hospitalised, and tried to apologise, in an attempt to mend what little remained of their original relationship, a part of her even hoping that he wanted to try it again, before he'd shot her apology down, telling her that she was apologising to the wrong person.

By the time she'd figured it out and apologised to Bobbi, Ward had 'died', and Arsenal was in his place, eliminating some of their more advanced SHIELD Agents like they were all rookies fresh out of The Academy.

Then he'd returned to eliminate them as a member of HYDRA, before Bucky - The Winter Soldier, of all people - had managed to help them cancel out his programming, and return him to normal. They had one week then, were she ignored him out of fear, before the senior agents had their impromptu party, and she had resolved to speak with him the next day.

And by then it was too late, he'd already left and told them not to look for him, and despite all her desires to, she had obeyed his wishes and not gone looking. They had expected something after his brother Christian was released from prison, with his sob story making his popularity higher than ever - and they waited for the story about a man wreaking havoc with his life, or even an assassination attempt - but after two months, there had been nothing but silence.

Feeling frustrated, she let her mind wander, and Jemma had used her moment of distraction to sweep out her legs, and she hit the mat, as her best friend squealed in triumph from above her.

Shaking her thoughts on Ward from her head, she took the offered hand and pulled herself back to her feet, preparing to go again.

Doctor Leslie Thompkins was a fifty-something, semi-retired woman, who had apparently been working, part-time, in Merlyn Global's Medical Research Department for nearly fifteen years, while operating a small, free clinic in The Glades, and she seemed to be every bit as excited about her work as he imagined she had been all those years ago when she had first started.

On their way up to the office of Merlyn Global's CEO, Malcolm Merlyn, he refused to feel nervous about meeting his boss, and listened politely as she explained whatever it was she was working on. He was paying attention to her, and adding in his own positive comments at the appropriate times, but he had stopped be able to understand what she was talking about, before they'd even left her work area.

All he knew, and needed to know, was that whatever was in the box he was carrying was important to the company, and that it was his job to guard and protect it, and if it became necessary, Doctor Thompkins as well.

They both continued to walk and talk (or just listen in his case), on their way to Mr Merlyn's office, before she abruptly stopped when his secretary waved them through. Leslie took a moment to compose herself, fixing her hair, and making sure her blouse was buttoned, before she marched in, as Ward fell into step behind her.

The office itself didn't 'scream' luxury the way some offices he'd seen over the years did, but Malcolm Merlyn had that air of affluence around him that only came from having more money than he knew what to do with. The way he walked and presented himself, even when sitting down, matched up perfectly with the several thousand-dollar suit, and the several tens of thousands of dollars' worth of Rolex that adorned his left wrist.

Leslie motioned for him to place the box on Merlyn's desk, so he did as he was directed, before stepping back against one of the far walls, observing them, and continuing to assess the view from several of the larger skyscrapers around them. There was always a possibility of an attack from a sniper rifle - especially when there was a company's classified material involved.

"You can leave us now"

Malcolm Merlyn's voice resounded through the room, bringing Ward's full attention to him, only to find his boss looking at him, sharp brown eyes piercing his own.

"That's quite alright Sir"

It was harder for Grant to tell who was more surprised, Merlyn or Leslie, but he could see the flickers of anger playing at the edges of Malcolm's face, while the doctor looked like she wanted to distract her boss so that he could escape.

"Excuse me?"

There it was. That dangerous tone he'd been waiting for.

"My job says that wherever that box goes Sir, I go. That's what you've hired me to do, so that's what I'll be doing. If that's a problem for you, then you may wish to review the security guards' standing orders"

Merlyn didn't seem angry anymore, he just had one eyebrow raised, and looked… impressed, an emotion that was noticeable in the way his voice changed.

"Well, how about that? I've finally hired a man of convictions. A man with a backbone. I could use a few more men like you… maybe one of you will rub off on my son"

That was the end of their little conversation, as Malcolm returned his full attention to Doctor Thompkins, and Grant resumed his scanning of possible nearby vantage points, checking for sniper rifles, reflections from camera lenses and scopes, and any other possible threats to his employer and colleague, taking the time to change windows every few minutes.

He continued his scan as Leslie and Malcolm talked about budget restrictions and rates of progress, doing his best to tone out as much of their conversation as he could in close proximity, given that it was both classified, and way beyond his level of understanding.

"-next time Doctor. Thank you"

Hearing those words, he knew that the meeting had come to an end, so he waited as they exchanged their 'thank you's and 'goodbye's. He noticed as another man, a few years below his own age, he guessed him to be early to mid-twenties, entered the room with an exaggerated swagger.

The typical pompous asshole.

"Oh hey Dad, good you're done, we need- Grant!?"

His gaze instantly snapped up to meet the newcomer, to assess him, but their eyes instantly met, and a surge of a connection flew through them, taking his breath away. Those deep brown eyes that matched his almost perfectly, but with a level of mischievousness he'd never had, but he recognised it, and he knew exactly who he was looking at.

The only person it could be.

When he had burnt down his own home at fifteen, he'd been sent to Juvie. As part of agreeing to go with him, Garrett had gotten Rosie and Thomas out of their home, away from their father, and into different families, but he never knew what had happened to them from there.

He hadn't wanted to know where they'd gone, or who they were with.

Not if there was even the slightest chance he could mess it up.

Now he knew, because across from him stood one man that he never thought he'd ever see again.

He could still remember the look on the face of the scared twelve year old kid he'd woken up in the middle of the night, and told to leave the room quietly, to not wake Christian and their parents, his voice, lined with pain and regret, managed to only get out the one word.

"Tommy?"