A mixture of Sonic universes old and new, but predominately based around the world of Sonic 3 and Knuckles, this story sees the rise of an Empire, the rebirth of an old weapon, and the final retaliation of a hero.

AN: Hi there! This is the first of a three part story which will be updated as I go. Initially I wanted to wait until it was all finished before uploading, but by now this damn thing has been stuck in my head for long enough! Concrit is always appreciated and I will likely go back and revise small parts as I go along, mistakes and inconsistencies and so on. This will take some time to complete, but I do hope you enjoy what I have so far and stick along for the ride. Thanks!

Prologue

"Doctor, are you… absolutely sure this is a wise idea?"

"Of course I am."

"But… y- your grandfather explicitly said that Project Shadow wasn't to be activated again, didn't he?"

A black ear flicked up at the sound of his name, as did crimson eyes. From where he stood in the corner of the office, the dark hedgehog watched in silence as the Doctor turned sharply away from the window and glanced, smirking, at the worried-looking man standing by his desk.

"Shadow," the Doctor then began, rather matter-of-factly, "is going to be a very valuable asset with regard to the construction of this ship- and indeed, the world as we know it! I've already assessed the possibility of a rebuttal and it's unlikely that he's going to cause many problems in the long run. Extremely unlikely, in fact."

This didn't seem to quell the man's worry, who looked over to the hedgehog in question before setting both hands down rather heavily onto the Doctor's desk, leaning forward as if to negotiate, or perhaps plead. The man was probably in his early to mid-fifties, but his weathered appearance and ruffled grey hair aged him by at least ten years. Age, tiredness and a cynicism born from many broken promises made by the Doctor was reflected in watery eyes, a grey-blue colour that was clear as glass. "But how can you be so sure of that?" the man questioned desperately. "Project Shadow was created as a weapon, Doctor, a weapon by a… by a scientist gone mad! Surely no amount of modification can change what he actually is?"

Deep red eyes flicked between the straight, army-like stature of the man and the rotund, moustached form of the Doctor standing only a few feet away from him. Black goggles hid the slight frown which contorted his features at the mention of a 'mad scientist', but otherwise, Eggman retained his casual optimism, and merely smiled. "The hedgehog's memory has been wiped clean, General," was his offhand reply, and he waved his hand dismissively. "Obliterated, if you will. The procedure was excruciatingly thorough for him and I can guarantee that he does not, and will not, remember anything before today. Nothing that was of any importance, at any rate. Gerald Robotnik – my grandfather - should be the one person he remembers."

Shadow remained silent and attentive. He was listening to this conversation intently and was certainly very much aware that he was the topic of their discussion. But nothing that they were saying about him really registered. Even as the Doctor then looked over to Shadow and grinned a sly, would-be suspicious grin, red eyes could only look back at him blankly. "Isn't that right, Shadow?"

Shadow thought, and felt, nothing. He recognised that he was being asked a question, and gave a small nod in response. "Yes," was his flat answer. Shadow made no other sound or movement. He'd been quiet for the entirety of their meeting as a matter of fact. Perhaps he should have felt something at the Doctor's mention of having his memory wiped, but even the words 'Gerald Robotnik' conjured only a vague image of a very old man, and no real feelings of recognition.

Even with this reassurance, however, and Shadow's seemingly calm exterior, the General did not look any less worried. Eggman stepped up to his side, then, and slapped a reassuring hand against his back. "I am not the same as my grandfather, General," he stated proudly, a note of cunning in his voice. "I am more, much more than him. How else would I have been able to construct this much without the help of the government? This world would been ruined beyond all help had I not stepped in all those years ago!"

At that, the General glanced to the floor, thinking, comprehending, regretfully acknowledging the Doctor's words. "Indeed, you have come very far in a very small amount of time," he was forced to admit, quietly.

"Without my development, the damage caused by Project Shadow so many years ago would have been irreversible… as I recall you saying." The Doctor's black eyes glinted, his red moustache bristling beneath a long grin.

"Yes. Yes, that's also true." What else could the older man say? Cornered by the Doctor's unfortunate truth, the General withered. "…Your grandfather and his creations left the world in a mess… it is you we have to thank for picking up the pieces when the world no longer believed in their government… in us. "

Something in Shadow prickled briefly, some kind of sensation along his spine. Apparently he had caused damage? Without thinking, the hedgehog glanced down to his gloved hands, observing the lines of his palms, the fabric creasing as he flexed his fingers. Had he really, in a past time, been the cause of destruction? It was not something Shadow could fathom, no matter how hard he tried to remember, and so his hands dropped, and his eyes lifted back to watch the two grown men at the desk.

"Well, then!" Eggman laughed heartily, hoping to prevent any more long spiels about his grandfather's past. "Don't underestimate me, General. And more importantly, don't let your trivial worries about an older mistake – indeed, a hedgehog of all things – stop GUN from investing in the Enterprise." Another reassuring slap followed this. "It's for global benefit, after all! All I need are just those external power sources, and development can begin once again!"

The General blinked at this, jolted out of worry as he was suddenly reminded of why he had been invited onto the Wing Fortress in the first place – to discuss GUN's co-operation in the rotund scientist's new scheme. Smiled, somewhat sadly, as he faced the Doctor and nodded his hesitant consent. "Ah, yes. Of course. Forgive me for questioning you, Doctor…"

"Not at all, not at all… it's understandable, I suppose. Now, about those chaos emeralds…"

As their discussion fell quietly into the final negotiations, Shadow allowed his attention to wander elsewhere – namely to the window beside him, where an orange sunset was casting a giant oil refinery in soaring black silhouettes, far off in the distance. Smoke poured out from the tops of shadowed pipes, steel-grey plumes rolling amidst clouds breaking over the setting sun, with the water around the refinery seemingly darkened despite the sun's reflection.

Shadow stared, lost for a moment in the striking colours. It was only the second time he had seen a sunset, and the vision of smoke from the refinery and the sun casting its pumpkin light over the sea almost looked like a still image. It was a beautiful picture, Shadow could certainly recognise that. And yet the sight of it, of smoke drifting over the half-set-sun, of black and orange so bright and dark in contrast left something inexplicably heavy inside him. An awful weight. An ominous feeling, which Shadow - being entirely new to this world – could not place. How could a sight so beautiful leave him feeling this way? It WAS beautiful, wasn't it?

Perhaps because there was nothing in front of the refinery but sea. Miles and miles, hundreds of miles of sea. A long, rippling stretch of water interrupted only by the black-silhouette oil refinery on the edge of the horizon. There was nothing beyond the refinery and nothing before it. Perhaps it was simply a few stray emotions confused after his awakening, churning around inside him, trying to find their rightful place.

Somehow, though again he could not place it, the sight of it bothered Shadow immensely. As though there was nothing, nothing but darkness to be seen ahead of them. His brows knotted together in a small, slight frown, still staring intensely at the view until the humans spoke up once again and broke him from his thoughts.

"Right, well then, if all the papers have been signed and settled… I will have the troops deliver the emeralds straight onto the deck for you tomorrow. As you know it's…. risky and I'm still not 100%, but I'm going to trust in you, Doctor."

The two men shook hands. Black ears flicked up and Shadow glanced back toward them, watching the older man smile weakly at the Doctor. Though their discussion had certainly concerned Shadow, it had not really been of concern to him on any sort of emotional level at all. The Doctor had already explained what was going to be happening, so whatever they discussed was really of no importance to the dark hedgehog.

The time will come, Shadow, when I will require your assistance for the benefit of this world, the Doctor had told Shadow, but a few minutes after his awakening. You have been sealed away for a very long time, but the time has come, now, to put you to full use – something that my grandfather, and your creator, never managed to do.. correctly, at least.

As such I will be bringing you with me onto my fortress, the Flying Battery, though it's nowhere near completion and I'm counting on you very much to provide help to the others working there. You see… the outside world isn't prepared for you yet…. Nor, for that matter, is it in any real state for any sort of inhabitation. So for now, working with me is going to be your primary objective until other things have settled. Is that clear enough for you?

The Doctor had been clear in his words but Shadow had struggled to understand what was meant behind them. He was on a planet known as earth, he was with someone he considered to be a relative, and apparently his purpose for existence was in the process of being realised. He had not been awakened without meaning, and so, Shadow was content to just accept everything he had been told even if he did not understand what, exactly, his purpose pertained to. He was new to this, after all. And all he could remember before now was the faint image of the earth from space, from the place he had originally been born in, and an old, sad, dying man who he presumed had been his creator.

There was a part of him, however, which couldn't help wondering as he looked out across the sea… exactly what had happened to the world – seemingly peaceful aside from the far-off refinery – that had made it so apparently uninhabitable? He had seen nothing of it for himself, yet; his bright red eyes had barely been open for 48 hours. All Shadow had seen so far had been the abandoned storage room from where he had awakened, the corridors leading up to Eggman's office, and then, the view from this window. Aside from the faded memories visible only to his mind's eye, Shadow had no idea what the world, outside this little sphere the Doctor had shown him, looked like.

It was not his place to question just yet, though. As it was programmed into him, Shadow had no choice but to accept what he had been told, and nod along obediently to everything the Doctor said. The personality still lost in decades of stasis and in the obliteration of all Shadow's previous memory was yet to break out, leaving the black hedgehog content in his quiet acceptance. Questions could come later, once he understood exactly what was going on.

"Then for now, General, let's head over to the Battery, shall we?" the Doctor then suggested, the hand on the older man's back guiding them both toward the door of the office. He paused then, turned around and gestured for Shadow to join them. The black hedgehog did so without a word, casting one last glance to the sea and sky and darkness, and then he stepped up to the humans, both his expression and demeanour neutral.

The worried blue-grey eyes belonging to the General met the unblinking, unfeeling red of Shadow, and the two simply looked at one another for one silent moment before the Doctor stepped between them. "Come now, you two, it'll take an hour or so and as I'm sure you well know I am a very busy man!"

With that, the Doctor hurried them out, and as Shadow followed quickly behind them, the General did not look back at the black hedgehog again.