Disclaimer: I own nothing, especially not any of the Doctors featured in this story. I just like to play with the toys, but I promise I'll put them back in the toybox when I'm through.

Author's Note:Although this story lists the 11th Doctor and the 9th Doctor as main characters, Doctors Eight and Ten are also heavily featured. So are several different companions from all four eras, not to mention the half-human Doctor. This is a multi-era saga of the Time War, in all its bloodiness and horror. You have been warned.

War By The Numbers

When something twinges the Eleventh Doctor's memory, he begins to realize that everything he remembers about Amy and Rory is wrong…and so are years worth of his memories.. Nothing adds up, and he finds he still has a part left to play in the war he thought he'd finally left behind. Here is the story of the Last Great Time War. Everything that was, everything that is, everything that must not be: a Time War in every sense of the words, death and destruction and loss in a non-linear form.

Prologue: Everything Wrong

Eleventh Doctor

"What is it?"

The Doctor took a long moment before answering, crouching in front of the small dark box, careful not to touch it even with his sonic screwdriver. It was shaped like a rounded-off "x" and thicker in the center, and so nondescript: gray in color, the "box" had absolutely no identifying markings at all. It was easy to miss amongst the rock and sand, and the malfunctioning perception filter still in place made the object even less obtrusive. According to local legend, it had been buried here on Daracia for centuries, having fallen from a burning sky in the times before living memory. Everyone had forgotten about the box until an earthquake had shaken the ground loose…and as always, the Doctor could not resist a mystery.

Especially when that mystery was currently disrupting the power supply to every building for miles around.

"I have no idea…" Another rotation of the sonic screwdriver proved useless; he was getting no readings whatsoever. According to his favorite tool, the box didn't exist. And even if it did, the sonic screwdriver insisted that it had no power source and was emitting zero energy. Not malfunctioning one bit.

But there was something ticking at the edge of his consciousness that warned him that he was malfunctioning. Just a bit.

"I've never seen anything like it." She crouched to his left, impatiently holding a clump of ginger hair out of her face with her right hand.

"Of course you have—you're a Time Agent!" The words came out automatically. Something blurred in front of his vision, but rapid blinking cleared it.

"I'm a what?" Amy asked.

"Hold on a moment. What'd you just say my wife was?"

The Doctor scowled, shaking himself. "Forget it. Senile moment. I'm old enough to have them."

"Right…" Rory trailed off doubtfully, but the Doctor ignored him, too. Or tried to, anyway.

He checked a sigh; so this was why he'd never brought a married couple around in the TARDIS. They always ganged up on him.

"Stop glaring at me, Pond. I can feel my hair burning."

"You're a giant baby," she retorted with a snort. But she was still crouched next to him, staring at the box in fascination. "Speaking of burning…?" she prompted.

"Burning?"

"The bloody box, Doctor. The one that fell from a burning sky. Have you ever seen anything like it?"

How had his attention gone elsewhere? This situation was growing stranger by the moment. "Well, now that you mention it, I don't—" Memory tugged.

Three Daleks meeting with a shadowed figure—one of them extended a pincher to accept a small object lined with fading golden lettering—

His memory was perfect; the curse of being a Time Lord. But this had always been fragmented. Only this. The one thing he could not remember completely, the one way to make a Time Lord forget…

A wall of row upon row of boxes, all glittering softly in the low light. Through a closed door, an orange sky was just barely visible—

"No."

He stared at the box, barely hearing as Amy asked:

"No, what, Doctor?"

His lips moved on their own. His eyes stared. "No."

"Doctor?"

"It can't be!" He jumped to his feet as the sudden burst of adrenaline hit, then caught himself and dropped down to all fours in front of the box, peering at from every angle he could think of. His mind was whirling, spinning, running in overdrive, fast even for him.

"Can't be what?" Amy demanded. Rory was crouching by her side, now, as fascinated as he was.

He wished they were as frightened as he was, instead.

"Every single one of these boxes was destroyed. Gone. Erased. Never existed." The Doctor leaned over the box, studying each side in turn. Again. Was that lettering he could see?

Was he shaking?

"Destroyed when?" Rory asked. "Isn't time like that? Can't things happen out of order, and this just be from before they were destroyed?"

Any other time, he'd have been impressed by the lad's brilliance. Not now.

"Not this," he answered heavily. Tightly.

Painfully.

"How's that supposed to work, then?" Amy chimed in.

"They were destroyed in the Time War," he replied in the tone of voice that usually warned companions to Ask No More.

She only frowned. "The what?"

"Don't ask."

"Well, be like that, then—"

"Hold on, I think I've heard of something like that," Rory cut her off, and though the Doctor did not turn to face him, he could hear the memory in that soft voice—and something inside him twitched.

Only once had the Time War peeked its way into the present, only once had they assembled enough power to try to break through from the past—but not like this, not now. Never again.

He wondered if the Master was still out there somewhere.

Not that now either!

Forcing himself to focus, the Doctor sat back on his heels and reached out a hand to brush his left thumb against the box's edges.

"Doctor—"

She sounded close to panic. Of course, all of the locals who had touched said box had collapsed into comas, but Amy wasn't fast enough to stop him…and he knew this technology. He didn't want to, but he did.

Golden-black script flared to life under his finger's tip, and a forgotten song filled his mind.

Orange skies burning red at morning.

Soft touches from mind to mind, flowing so quietly and carefully, but always, always there. The full feeling of knowledge and wisdom and ageless time, arching out across each universe and binding together even those who ran away.

There was no running from oneself, after all. The togetherness always followed, the sharing of something larger than a mind, something greater than memory and longer than life. Always part of something greater, even if something crumbling and forgotten, greater and older and more magnificent than any single soul…

Sweeping mountains, memories, mel—

Crack.

He was still distracted by the sudden influx of images when the ground dropped out from under them.

"Rory—"

Crack!

Despite his preoccupation, the Doctor almost got the word out quickly enough. "Loo—"

But he was already tumbling to the—beneath the?—ground and Amy and Rory both yelped in surprise. Rocks crashed down around them; something bounced off of the Doctor's left shoulder and made him hiss in pain. Dust thickened the air enough to make his respiratory bypass system kick in as his companions coughed and choked somewhere off to his right. They didn't sound above him, so they must have fallen, too—his sense of time was sluggish, but beginning to cope with the sudden (and slight, though unexpected) spatial shift. A long moment passed before the Doctor was able to suck a breath in.

His throat burned, and the air tasted unbelievably stale and sour, as if no one had been there for hundreds of years. I'd forgotten how much using the respiratory bypass system hurts. It's been…

He wasn't going to think about that now. He so wasn't.

"Doctor?" Amy coughed again.

"I'm here." He scrambled to his feet, waving a hand in front of his face as the air cleared. Moving to take a step towards his friends, the toe of his right shoe hit something with a clink, and the Doctor bent to pick the box up without thinking.

This time, he was better prepared for the sudden onslaught, but his mind still filled with awareness, knowledge, and…memory.

The brilliant Untempered Schism, the window to time and the universe—every universe—beautiful, deadly, inspiring, maddening—

Footsteps on cool floors, Romana's frightened white face whispering "No—"

Time sweeping through the ages, faces, names, knowledge, peace, love, war, madness, eternity—

Everything and nothing, nothing and everything—

Gasping, the Doctor forced the connection shut. He almost didn't, and certainly didn't want to, but now was not the time. Still, he had to swallow dryly; the sudden quiet in his mind hurt. A second deep breath buried the pain.

You should be used to it by now, Doctor. It's been years since Gallifrey burned. His own cynicism sounded forced, even in his own mind.

"Doctor?" He could see Rory's vague outline through the gloom, now. "Where are we? And what is that thing?"

Brace yourself. Smile because you have something to hide, and then temporize. It might as well have been the motto of his life. Throw so much knowledge at them that they never miss the lack of answer. "Well, judging from the fact that we fell downwards and the sky is above us, I would venture to say that we're underground. Logic follows that we didn't fall up, after all; this planet has gravity close to the intergalactic standard."

Amy scowled at him. "Load of help you are, Mister Obvious. And you didn't answer the second question."

His forced smile froze on his face as his left hand tightened on the box. Despite himself, the Doctor had to glance down.

"This…?" He swallowed again, braced himself. "This, Amy Pond, is a memory module." His left hand trembled, and he hoped she didn't notice. "From the Matrix. On…Gallifrey."

"The Matrix? Gallifrey?"

His eyes slid shut, and the Doctor found himself clutching the box to his chest. His voice was hoarse, felt old and raw. "The sum of all Time Lord knowledge and memories…housed underneath the Panopticon and protected above all else. To breach it without permission was treason, to tamper worthy of death."

He sucked in a deep breath before answering the second question in a whisper. "And Gallifrey was my home."

He'd thought this regeneration was past the Time War, past the pain and the loss and the horror of it all—he'd been grateful that his memories grew more muddled by the day. But confronted by the past, all he wanted to do was cry.

A long moment of silence passed before Amy asked quietly, "And this… module thing was a part of that?"

"A part?" He opened his eyes with an effort. "Oh, no. Not a part. It's Time Lord Science—it's bigger on the inside than the on the out—"

Flash of memory. Screaming—

Without warning, his right hand moved up to touch the module and the walls the Doctor had constructed between it and his mind collapsed. He couldn't help it; suddenly, the need to fill the silence was overwhelming.

I'm supposed to be past this!

He stood in a rapidly clearing passageway, with rows of metal doorways to his right and left—cell doors!—stretching on for hundreds of feet. The heavy doors were quadruple locked, deadlock sealed, and alarmed; power conduits stretched into and out of every cell—

Was this memory or reality? The Doctor blinked rapidly, but his usually logical mind couldn't wrap itself around the situation yet.

He could hear thousands of voices screaming in pain, stretching across the entirety of time and space—what ought not happen would now always be, and the uneven chorus stretched across the ages, collapsing his soul under the weight of such agonizing desperation and agony. His knees shook, buckled; every sense was alive and feeling, and his mind was no longer empty but filled by this beautiful horror.

One voice was screaming louder than the others, closer—

Hands were on his shoulders; Rory was shaking him. "Doctor!" He blinked once more, staring at his worried companions blankly. From somewhere he got the impression that they'd been trying to get his attention for some time. "Are you all right?"

"I—all right?" He shook himself. "Well, um, no. Not really. But that's to be expected."

Flash.

The same type scene with glass walls instead of heavy metal ones, glass that was not made of glass. Soft screams and the inevitability of loss—

Crack. His face stung.

"Oi! You. Pay attention," Amy demanded.

"You slapped me," he gaped, his attention now fully on the present. The last part had been memory, but the hallway of metal doors was real. They were standing in it.

"You bet I did," she gloated.

"You looked like you were about to pass out," Rory clarified apologetically.

"Oh. Well, thanks then."

Amy wasn't convinced by his smile, though, and Rory didn't look like he was either, but the Doctor's mind was elsewhere, clinging to the now-suddenly-quiet and dying song that had once so thoroughly broken both of his hearts. His mind had been silent for so many years (thirty-seven by the calendar of Gallifrey he still used, for some reason, to track time), and now the song he heard was the heavy end of the Time War, the screams and the deaths and the destruction of everything—

It was only an echo, but it made him want to scream.

And there was something wrong with it, too.

"Doctor?"

Her soft voice was so very far away, and her features blurred into a ginger-rimmed blob before he closed his eyes to keep back the tears. Only an echo, he told himself harshly. Only. An. Echo.

Spiral backwards in time. It hasn't always been right; things have been more wrong than you realize for quite some time. Something overlaps, somewhere, and your conscious mind ignores it because the timelines don't compute, even for your massive Time Lord Brain.

You know it's wrong, but you don't know when. Why.

Two sets of memories are warring for control, and in your mind, that's Impossible. Not impossible of the breaking-the-walls-down-between-two-universes type, either; this is Impossible, two things that cannot coexist in the one timeline that is only one timeline, in the last war of a doomed people.

Rassilon wasn't there the first time, and you're not even positive that monster was Rassilon. Something isn't right, something going all the way back to the Medusa Casade when you were just a boy.

River knows. Or she knows a part. Is it because you go to her after all of this clears because she's someone you can trust, someone who does not look at you with wonder or with the need for guidance. She's as close to an equal as you've had since—

Tenth Doctor

Bad Wolf Bay.

The mostly-human Doctor turned to the all-human Rose with tears in his eyes. "Well," he said softly. "This isn't exactly the future we hoped for, is it?"

She remembers, now, and so does he. Her voice is choked with tears, both for the man he was, the two men he now still is, and the ways she learned to love them both. "Not really, no."

They're both thinking of orange grass and red skies, of warm embraces and chances taken and not. Of lessons learned and wars fought.

"I'm so sorry," he whispers helplessly. "I killed you."

A/N 2: Thanks for reading, and please do review! I've got the first 8 chapters written, so the more motivation I have, the faster I'll write.