Disclaimer: Chapter 1.

Thanks dannybates and servantofclio for pointing out that I posted the wrong bloody chapter! Oy vey, my brain!

These chapters are coming out SO MUCH SLOWER than I originally intended. By, like, a lot. Oh boy, I'm so sorry guys. Promise I'll try to speed up. The whole point of this is to show that a different ending is possible with little time and effort. Unfortunately, the writing time required is going to have to be waved; I am but a fanfic writer who has two other jobs, neither of which includes writing.

Hell, Bioware managed to make their Extended ending before I even got this far. Incidentally, I do feel the new content improves it and they did as best as they could with what cards they dealt themselves. Still don't like the writing and think it's silly, but it doesn't feel so rushed, anymore.

Chapter Two – Family

"You are indeed family. No other could have lived to oppose me in person. Of course, it will not matter in the end. Ultimately, I will prevail, and a new era will be born into the Realms." – Sarevok Anchev, Baldur's Gate

Hackett left the console and went towards the display of the battle that was taking place just outside their own bulkheads. "What's the status so far?"

The pilot didn't even look up as he worked the displays. "Three geth fighters filled in where a turian dreadnaught tried to punch through towards the Citadel. They were destroyed by the Reaper."

"And the Crucible?"

"Nothing yet, sir."

Hackett went silent, taking the moment to let the coil of tension run past him. This was a hell of an unprecedented situation, and he still wasn't sure if the reality was going to come crashing down that this is it. He was seeing something before his eyes that was before something he only knew academically.

Ships of all forms and sizes, fighters with various amounts of damage zipping or limping, Reapers kiling, Reapers conquering, Reapers falling from the sky. Fire and shockwaves and hulls bursting, cracking, falling apart. Each burst in the battlefield represented lives lost or lives saved, and the battle was both lost and won until the Crucible came on or was destroyed. Everything he knew was being unmade.

He was seeing Armageddon before his eyes, and he willed the weight of such an impossibly heavy situation didn't crush him for just a little longer. "Looks like we have a regular Schrödinger's box, here."

Shepard woke with a million nerve ends in her skin screaming at her in pain. Somehow she only grunted in turn and tried her best to twist and turn away from whatever was trying to pull her flesh off, but hands were there to keep her from struggling. Wrenching away from their grasps brought more pain, but with the pain came clarity. The dark clouds in her vision faded and allowed her eyes to focus.

The owners of the hands were many: an asari, a human, a batarian, and… something she didn't recognize off hand. They murmured low with little enunciation, and some of the speech was outright glitching. It all flowed on top of each other without hesitation and none of the words seemed to have anything to do with how they were scrabbling to continue pulling charred bits of useless armor from her.

Those damn images from the prothean beacon came flooding into the forefront of her mind, and she felt like she was falling and unable to breathe. The passage of time didn't register. She remembered an old vid she saw once of a girl dropping down a dark shaft as hands from all sides both slowed her descent. Which way do you want to go? Up or down?

Shepard gasped and forced herself up again.

The crowd around her had dissipated, and a few continued to mumble as they worked some sort of tubes into the container she had been laying back in.

A collector coffin.

She pulled herself out with a groan, finding that, though she was neither in her armor nor nude, whatever her body had been covered with stuck with the sides of the coffin viciously. With all her strength, she pried herself from its walls. She was surprised she didn't feel so much pain as a result. She had been heavily wounded earlier.

The two mumbling creatures working with the tubes, neither of them of any race she recognized, reared up and set wide eyes on her. An instant later, there was a pulse in the room that felt like it was coming from... everywhere. The immense pressure of it knocked her down onto her knees, and she heard the tell-tale droning blare of a Reaper within it.

The two aliens, however, seemed to gain strength from the pulse. Then, they spoke, in unison, with such force that the words seemed to come from outside them. The syllables she could not parse—except "SHEPARD". Their eyes gave the unsettling glow of indoctrination.

They approached, but Shepard was still able even while they might have the immediate upper hand. She used their charge to her advantage and struck low, to their abdomens, and shoved them backwards. Before they could recover, she spotted something she could work with; there appeared to be a ledge through the door behind them. She took a run forward and shoved one, succeeding in pushing them over. The other, advancing to her rear, had a similar fate when she flung it over her shoulder. She watched and examined where they fell, and finally took in her surroundings.

Low light, seams sliding organically into the walls instead of the blocky bulkheads of most ships' inner hulls, cords slung and connected from area to area like umbilical cords… she'd seen a place like this before. Formed instead of constructed. The derelict Reaper.

She was inside a goddamn living Reaper.

And, in a level below her, where she had thrown over the unknown creature, there were dozens more milling about, some like what she'd just encountered, some familiar, and some she'd still have yet to have seen before then.

Suddenly, it made sense. The pulse from earlier felt much like when she'd encountered Project Rho, except she felt that energy specifically from the artifact. Here, the electricity was prickling at her from every angle. These aliens—whatever they were—were no doubt indoctrinated slaves of the Reaper she was inside. Damn, hell of a setback.

At least, if nothing else, the ruined armor from before was off of her, though what she was now clothed with looked too close to Collector skin for her comfort. Similar to the armor she collected in her campaign against them so many months ago. Add to that, she felt much better. The Cerberus-issued implants must have done their work in restoring her, though she was far from full functionality. At least that was something the Illusive Man succeeded in.

And in that was another sliver of Good News: Though she didn't have an omni-tool or any other proper equipment, her various subdermal implants were certainly still exactly where they were, including her communicator. She fired it up, hoping it could work without amplification or a signal reroute. "This is Commander Shepard of the Normandy SR-2. Requesting radio check."

Static.

"Anyone on this frequency—this is Commander Shepard. Is anyone out there? ...Damnit!" Not so much luck. And here she was, unarmed and dubiously armored, standing in a ship that was redefining the term "hostile territory", and she had no contact with anyone out there, or even any clue as to what was happening.

The only way to go was forward, so that was where she went. Still not at a hundred percent, she limped through from room to room, seeing increasingly startling images of people—asari, humans, batarians... others—behind glass-like surfaces or in the distance on other catwalks performing various repetitive tasks, most of which seemed to be pointless. The layout had an eerie glow and everything pulsed with a distinct and very wrong life. Or maybe that was just how the light settled on these disturbingly organic structures.

A gun was most likely out of the question, so she had to be careful. When she came to a long hallway of indoctrinated people, her only course of action was to duck down into a crawl space and hope that she didn't get lead into live wiring or a trash chute.

"Protect… waiting for more informa… looks like Hell through here, bu…"

A voice, distorted from the surrounding static, cut through on her comm as she moved. Her heart skipped a beat, though it was obvious from the chatter that communication was going to be difficult. Still, at least someone was going on out there. Maybe when the signal improves, she'd be able to reconnect with brass and work out something from in here to their advantage. After all, she was as deep in as they can get.

As far as she could tell, maybe her progress was improving the comm. feed. She might've been in a part of the Reaper that blocked errant waves, and could be going towards an area more naked to the signal.

It was worth a shot, and if that wasn't incentive, nothing was. "Anyone on this signal, this is Commander Shepard."

Someone seemed to hear her, but it wasn't clearing up. She couldn't make out what the voice was saying. When it looked like she was coming towards an end to her cramped tunnel, she hurried as best she could and pulled herself out into another room. The lights were too low to determine anything, but there was no movement.

The static managed to clear up exponentially with her new location, and she repeated her inquiry.

"Commander Shepard?" a familiar voice called, "Damned if you weren't the last person I expected to hear. The extended comms are filled with chatter; I can't manage to get to anyone outside to help. You don't suppose I could give you my position so you could lend a hand?"

"Is that you, Bailey? I'm not sure I can reach you from my location. I don't even know if we're in the same arm of the galaxy."

"Well, this channel is a local one, so you can't be too far."

"Local?" Shepard's thoughts were interrupted as she registered a flickering of light to her left. She clamped her mouth shut and turned, seeing that the nearby wall had some dull, yellow illumination from inside a pod-like structure. It hit to her something of familiarity, but she couldn't really place it.

Behind the glass, she could see a form within the low light. It was strange and hunched over, much of it's body covered with wires and tubes, but she could make out shoulders and a head.

And a face.

Eyes opened and sprang to center on hers, and the scream of some strange, bird-like animal ripped ripped from its opened mouth and was muffled by the structure surrounding it. Its alien hands rose and scrabbled at the glass around it, pounding and screaming something unknown to her translators. Forms within lights all around her woke up with the commotion, and each added more and more of their own howls and cries until the sound was deafening. She turned this way and that, in a defensive stance, her heart racing as she realized what this was.

Whatever these aliens were, they were to be harvested. Their purpose here was to be liquefied into genetic goo, just like the humans abducted from the colonies by the Collectors.

"My god… they're making another one! And hiding it in another Reaper?" She leapt forward and tried to pry off the lid of the first one she saw. The thing inside, whatever it was, saw her attempts and shouted in a low croon, clawing at the side she was working on. Whatever it was, whether or not it was dangerous, Shepard reasoned, it didn't deserve to be processed into a Reaper.

A pressure slammed down on her from all sides, along with the blare of a low voice. "SHEPARD."

She groaned and buckled under the pressure, but did not fall and managed to prop herself up against the yellowish glass. The creatures within the pods moaned in similar anguish. "Harbinger," she said back at it.

"YOU WILL NOT ESCAPE YOUR ASCENDANCE, SHEPARD."

"Of all the pregnant Reapers to be inside, it had to be you." Her feet steadied and she managed to pull herself up, then went towards what looked like an exit. "But I've still got shit to do if you're around, so I'm not about to stick around to chat."

"SHEPARD HAS BEEN LOCATED. CAPTURE ALIVE IF POSSIBLE."

Before she knew it, she was sprinting through hallway after hallway of groaning unknowns locked in processing pods. Walls shut in on her and forced her to change direction. Various beams and whatever rose up under her feet to trip or trap her, making her stumble and only able to keep balance for her momentum. Indoctrinated creatures of various races descended on her in flocks. Their hands grabbed and snatched at her incessantly. They chased her and the natural biotic of asari flew at her and threw her against walls, but she managed to pull herself up and move on.

"Shepard! I think I'm able to track you down based on your signal! It's not easy but—holy shit!"

"What can you give me here, Bailey?" A salarian popped up in front of her and she managed to grab him by the horns and slam him into a wall. "Because I could really use a little back-up right about now."

"You didn't tell me you were right next to a goddamn Reaper!"

"Next to? I've got some news for you… damnit!" Her trajectory led her to a dead end. She whipped around to look at the approaching indoctrinated hoard, trampling over each other like a living wall.

She didn't have time to make her peace, because an eruption of sound came with the flooding of light as the wall behind her tore away. A powerful, black-blue energy surrounded it and pulled it away like it was taffy, and the whine of metal being ripped echoed before it was flung into the brightness. Without a thought, she leapt blind into the opening.

The drop was several meters and the landing was hard, even with the roll. In a second, Bailey was at her side and pulling her to stand. "You alright there?"

"Working on it." She looked up to the make-shift door.

Of all people, it was Aria, Queen of Omega, floating above and eradicating the whole group of hostiles with her biotics for all she was worth. Shepard couldn't help but gawk in confusion.

With a final grunt, she pushed the remaining away and landed next to the two watching, smiling despite herself and what looked to be some very obvious wounds. Maybe she enjoyed getting her hands dirty from time to time. "You know, Shepard, people really don't know what they're talking about when they label you as 'unpredictable'. Go where shit's hit the worst and there you are, right in the middle of it."

Shepard found herself grinning as well. "Strange as it is to say, it's good to see the attacks on the Citadel haven't brought you down."

"Like hell if I'm just going to roll over and die while Cerberus still has my rock."

That bit about the shaft of hands is referencing a scene from "Labyrinth".

This chapter requires a little more development than the usual level building, particularly in inventing new aliens. But the aliens in question aren't necessary to the plot or gameplay other than being different, so development could be as minor as taking pre-existing models and shapes and messing with them.