A/N: I don't know if you, like me, were deeply upset by the end of Assassin's Creed 3, but I felt the need to write an alternative ending, since it's pretty clear we won't be seeing any more of Desmond. I was quite attached to him and damn it, it was a such a pointless waste! All his training in the Animus, assimilating the skills of his ancestors…I would quite like to see a story where he survives and goes on help the Brotherhood in the present day with his mad skills. :P Anyway, that's a tale for another time. Read on!

Disclaimer: Don't own it.

Rebellion is in Our Blood

Chapter One: Life

Trapped.

It was a horrible, sick feeling, fluttering in his chest, as if his heart was being crushed under the weight of the pressure. The heavy, leaden pressure of this impossible decision.

Desmond stood in the centre of the room, while the shades of two Goddesses prowled around him, golden and shining and deadly, while his fellow Assassins stood struck dumb by the power radiating from the very walls of the room. He knew, in some indefinable way, that they could feel it beating against their skin with the strength of the summer sun, white heat shimmering through the air and making it difficult to breathe, let alone think.

His thinking on the other hand was mercifully clear. Or perhaps not, depending on how you looked at it. Desmond could feel the heat sliding around and over him, sensing the power but remaining untouched. It was as if he was made of ice, radiating cold and chilling the air immediately around him.

Protected.

The word rang through his mind and he knew it was true. Protected like Altair, like Ezio, whom the Apple could not touch. He had been fortunate enough to have the right bloodlines, to inherit the right genes – to inherit First Civilisation genes.

But for all that, he was helpless to actually do anything. Desmond's hands curled into fists as he watched the two otherworldly figures argue over the future of humanity. The resistance granted by his blood was passive. He risked a glance at his father, at Shaun, at Rebecca. They stood, mute and unmoving in the presence of the power of The Ones Who Came Before. He couldn't extend his immunity, couldn't protect them from the overwhelming power of this room. He couldn't find a single goddamn solution to this mess that didn't involve the destruction of the world – either instantly, via a solar flare, or a slow death at the hands of Juno.

Desmond ground his teeth as the two Goddess-like beings finally fell silent and turned to face him. And of course, Juno had planned it that way. This eleventh hour decision was orchestrated by her so that they didn't have time to find another way, to work out how to activate the towers themselves. Because Juno was the only one who knew how. Minerva had known, once upon a time, but millennia of residing with the Grand Temple had given Juno the time she needed to twist the machines into something only she could operate.

"Free me." Her golden eyes burned into Desmond. "And I will save the world."

And enslave it.

Desmond bit his lip hard enough to draw blood, barely noticing in the midst of his internal agony. Release Juno to both protect the planet and subjugate it? Or allow the solar flare to burn away the world, leaving the last dregs of humanity to begin again from the start of the cycle?

He took a deep breath and forced his mind into stillness. Think. Which is right? Which is the best decision for everyone? Because the whole world will have to live with whichever I choose.

He thought of the world. Thought of it burning. Thought of the collective knowledge and history of the planet, lost, of humanity beginning anew again. But most of all, he thought of the billions of lives that would be lost and the mere idea of it was enough to make him feel sick with horror.

My first instinct is to save. Desmond closed his eyes. Can the world live with the alternative then?

The thought of humanity being subjugated, stripped of all freedom and yoked to the will of another was enough to ignite a blaze of anger and pride within him, an instinctive rebellion; every fibre of his being thundered a resounding NO! It was enough to stir the ghosts of the ancestors who slept within his mind and their voices mingled in his head, a furious and defiant chorus. I bow to no one!

And so I am left with the same impossible decision. Desmond had to resist the urge to drop his head into his hands. Then a thought dawned upon him and the sudden blaze of hope that accompanied it was almost painful in its intensity. Unless…unless…

Humanity would not just lie down at Juno's feet and accept her rule. Was his instinctive reaction to the idea of enslavement not proof enough of that? Was history not proof enough of that? Rebellion was in their blood. Even when the First Civilisation was at its height, even when the Pieces of Eden controlled humanity's very thoughts, Adam and Eve had managed to break free and instigate a rebellion that had rocked the older race to its foundations. And the very fact they had been able to do so proved that the First Civilisation's methods of control were not absolute, not infallible.

Desmond opened his eyes, filled with new determination. Better to save the world and allow the human race the chance to fight back, than condemn it to oblivion. Where there's life, there's hope.

"Enough!" The two glowing figures ceased their argument and turned to look at him. "The decision's made, Minerva." His tone was enough to tell her his choice.

The Goddess looked both taken aback and dismayed. "She will enslave your kind, Desmond. Is this not why you fight? Is this not why you came here? To ensure not just your race's future, but also its freedom?" Minerva implored.

She doesn't understand. "Minerva, whatever Juno's planning – however terrible it might seem today, we'll find a way to stop it. But the alternative – what you want – there's no hope there," Desmond tried to explain, to make her understand. Juno was looking at her too, a terrible smile gracing her lips.

The other Goddess drew back and Desmond could see at once that he hadn't succeeded. "If you free her, you'll be destroyed."

He could hear the undercurrent of desperation in her voice and knew she had appealed to his sense of self-preservation as a last resort. It didn't touch him though. He couldn't explain it, but as soon he had seen the pedestal, he had known that to touch it was to die. Maybe it was one of the many stolen memories he possessed; maybe it was merely the uncanny instincts he had inherited from the First Civilisation. Whatever the reason, he had known that he would not survive this decision.

One life for many. Seems a fair trade. He ignored his own fear, drawing on years of practice – many of them not his own – to push it down deep. It didn't matter. It was a knee-jerk reaction to the thought of dying; his survival instinct kicking in. There were more important things than stake here than his life.

"It will happen in an instant. There will be no pain." Juno retorted, cutting off Minerva's last ditch attempt at changing Desmond's mind, not even looking at the other Goddess. Her voice was coaxing as she gazed earnestly at Desmond, but her golden eyes were bright with an undisguised, almost feral eagerness. She knew she had won.

"You mustn't!" The desperation was clear in Minerva's voice and the sound of it made guilt shoot through Desmond. How could he convince her? How could he possibly convey his certainty that humanity would not willingly submit to Juno, that they would not go without a fight? He couldn't – he hadn't the time. The thought nearly made him laugh, in that horrible, choked, half-hysterical kind of way. Lack of time was the whole damn problem in the first place. In the end, he just said gently, "It's done, Minerva. The decision's made."

She backed away and when she spoke, her voice was breaking with emotion. "Then the consequences of this mistake are yours to live and die with." Minerva flickered out of existence, hazing into gold light and then into nothingness, followed by Juno, still wearing that terrible smile.

Desmond turned to his fellow Assassins, who blinked and appeared to come out of their daze a little, as the power of the Precursors faded slightly without their direct presence. His father's gaze in particular sharpened as Desmond began to speak. "You need to go. All of you, now. Get as far away from here as you can –"

"Come with us!" William Miles interrupted, grabbing him firmly by the shoulder. "We'll find another way, it doesn't have to be like this –"

Desmond looked down and swallowed hard. For a moment he wanted nothing more than to agree, to flee the Grand Temple with his father and his friends. But he had made his choice. Humanity lived or died today depending on his actions and he would not run. "There isn't time," he managed to say. "You know that."

William looked torn, anguish and defeat warring on his face. He knew. "Son…"

If anything, the lump in Desmond's throat got even bigger. He gently pulled his dad's hand from his shoulder and gripped both of his forearms tightly, trying to convey both emotion and urgency. "You know it's true. It's already started. I need to do this now. Go, quickly." The pulse of Juno's presence grew brighter again behind him and William's expression became dazed again. "Go!" Desmond urged, giving his father a gentle shove. "You need to go!"

William Miles stumbled away, as if in a dream, Rebecca and Shaun trailing after him like lost sheep. Then they broke into a jog, and then a sprint, Desmond's words turned into a command by the power saturating the walls of the temple.

He watched them until they were out of sight. And suddenly there was nothing left to do. Nothing left except that final action. Desmond took a deep breath, stilled the tremors in his hands and ascended the steps to the pedestal. The Eye sat directly before him, the sphere glowing with a soft white-green light. His touch – the touch of someone with a remarkably high concentration of First Civilisation genes – would release Juno from her prison. He could sense her, close by though unseen. Her anticipation was like an electric charge in the air, waves of heat and power buffeting against his ice.

She is the reason for all of this.

Desmond was suddenly aware of just how much he hated her in that moment. He hated her for her manipulation, stretching across space and time. He hated her for withholding the knowledge of how to save the planet. But most of all, he hated her for forcing him into this choice. The decision was his; but it had been her options. He could only hope that after he was gone, humanity would be able to walk the third path he had seen, a path constructed solely of willpower, of the pride and resilience and the fierce instinct in humans that time and time again had said no.

I hope you give her hell.

And his hand came down on the sphere.

A/N: I suppose you could consider it canon up until this point, apart from a few minor dialogue tweaks. :P I've already finished this story, the rest just needs a few edits and will be up ASAP.