This started out as a prompt on the Kmeme:

Let's say for a moment that the Collectors are successful in capturing Shepard's body after the destruction of the SR1. They of course do the sensible thing and take his body back to their base and throw him into the Reaper they just finished building, using the Commander as the "Heart" of the new Reaper, choosing the Paragon of Humanity to form the deepest core of of their latest Harbinger class Super-capital.

In hindsight, this was not the wisest of moves.

Prologue

The first thing he heard was hissing. After than, a barely audible thrum that felt like it was vibrating through his bones. It felt like he was drugged and strapped down. His eyes stubbornly refused to open. The last thing he remembered was blacking out from a cracked O2 hose over Alchera. What had happened? The Normandy had been the only ship in the system, so who had picked him up? How long had he been out?

Suddenly, it was as if light flooded him from all angles. It disoriented him for what felt like a few seconds, but soon he could 'see'. He was in a room with sickeningly organic sections melded onto bare metal. So, not a hospital. Or not one that he'd ever enter willingly.

Then he looked down. Tiny creature scuttled around him. He looked harder, and it was as if his vision zoomed in. The creatures looked like insects, but he'd been wrong about their size. They were the size of humans. Which meant...

It wasn't a room. It was a cavern. But if so...

He then tried to look further down at-.

No.

No.

NO.

Black metal, shining with a strange iridescence. Sinuous curves. There was nothing human about it. In a rush, he knew what it was.

Something had made him a monster. No, a Reaper. How and why didn't matter. It had been done. He did the only thing that he could when faced with it. He screamed.

"NOOOOOOOOOOOOOOOOOOOOO!"

Plates opened and a beam lanced out, blood red, cutting through the wall the cavern. He thrashed around in what had to be his moorings, tearing giant chunks out of the walls and raining them down on the creatures below.

The cables holding his...body? hull? snapped with his exertions. Through the hole in the wall, he saw open space.

It was instinctive. Low level processes maybe. Whatever it was, he knew how to get away. More beams flew out, blasting a larger hole for him to crash through. The stone and metal scraped against him as he pushed through. Once out in space, he was assaulted by a cacophony of input. Heat, noise, chatter. He hunkered down inside himself, and the noise went away. He ran through the wrecks of countless ships, through the defenses, towards the relay he had found. The pinpricks of small beams against him, the bullying of wrecks out of his way - none of it mattered. Only escape, before these things could cocoon him again.

Moving faster towards the relay. It lit up like a Christmas tree when he neared, and he felt an echoing heat in what felt like his stomach. Closer, closer, and then blessed silence when he finally fell through it.

-ooo-

When he finally awoke, he was drifting through the gas clouds of a nebula. It was..peaceful. After a time, he came back to himself. Time to take stock. He wasn't supposed to be awake yet, of that much he was certain. Those...things, servants of the Reapers maybe, hadn't expected him to be aware. Maybe they had planned to finish indoctrinating him later. Maybe it hadn't taken. There were no voices whispering in his mind. Whatever the reason, he was sound in mind, if not in body. Speaking of which -

He turned his gaze inward. Yes, a Reaper shell. But not a complete one. He could feel things missing, like an empty ache inside him. He could..remember things, things he had no business knowing. They had to have installed... data banks, he supposed. But they weren't complete. History, where the Reapers came from...oh. Oh no.

Where the Reapers came from wasn't in his memory. How they were created was.

Thousands. Hundreds of thousands of humans had been melted down to create this Reaper. An evil synthesis of man and horror of it stunned him for an incalculable time. A great loathing welled up - was this what they had planned for the rest of humanity? Was he going to be encased in a shell of dead men, women, and children for all eternity?

No. He would not let this define him, change him. The Reapers would not win that easily. Mourn the fallen, yes, but then pick yourself up and continue the fight. Rage against the dying of the light if you need to, but never fall. Never falter.

The mission hadn't changed. Just the particulars. Stop the Reapers. Save the Galaxy.