Running Silent:

Ruins and Broken Things

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An alternate ME3. Commander Shepard and her team are on the run from Cerberus and trying to make alliances before it's too late. In a galaxy with no reaper kill switch, how can they hope to defeat something so ancient and powerful? Their last hope is a desperate plan that may cost them everything. Shepard/Garrus, other side pairings.

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Disclaimer: This author in no way profits from the writing of this story. All characters, dialogue, or other referenced material from the Mass Effect trilogy belong to Bioware.

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A/N: Hi guys, I know it's been forever. Real life got crazy busy. My husband and I bought a house! The day before we closed on the house, a fire sprinkler caused significant water damage. So when we moved out of our apartment, the house wasn't ready. We're currently in an Airbnb waiting for the repairs to be complete. Needless to say, the last couple of months have been complete insanity. I hope to be able to update regularly (about once a month) again now.

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Shepard smiled at Liara from across the shuttle. She wasn't sure the asari had stopped vibrating with excitement since their vid call, nearly a week ago.

"Ilos, Shepard!" she said, voice husky with fervor. "I want to go with you. I can help."

Shepard grinned at her old friend. "Of course," she said teasingly. "I wouldn't dream of going without my prothean expert." Neither of them could temper their smiles at the idea of one more mission together.

"Pack your bags, Liara," she ordered, eyes bright with excitement. "We're going hunting."

The asari fidgeted in her seat, jumping up the moment the shuttle touched down. Shepard motioned for Liara to wait as she stepped into the cockpit. "Why are we stopping, O'Connor?" she asked her new shuttle pilot.

"Bunker's closed," he said, motioning to the view on the monitors.

Shepard was hit with a sense of deja-vu. She stepped back into the hold, smiling wryly at her companions. "Well, Garrus, I hope you remember the way to the control switch."

The three of them stepped out into a wild but familiar landscape. Shepard's eyes followed the lines of the stone carved buildings, eroded by time and nature, covered in the grasping green plants that had grown around them. The air was still.

"Huh," Garrus said. "It looks exactly the same."

"It has stood for fifty thousand years," Liara replied quietly. "The time since we have been here is insignificant in comparison." She gazed around in obvious awe of the ancient, broken world.

"If I remember correctly, we need to go this way," Shepard interrupted gently, reminding them of their task.

"Oh!" Liara pulled up her omni-tool. "Here."

Both Garrus and Shepard's omni-tools lit up as they received Liara's file transfer. The commander raised her brows as she opened it. "You have a map of this place?"

"After the Normandy… after you…" She faltered. "I was invited to be a part of the council's investigation here, such as it was." She typed in a few more commands. "There. Our maps are synced. The control station is here," she said. "I'll mark the quickest route."

They moved quickly into the eerily quiet complex. An unsettling feeling grew stronger inside Shepard with every step. The ground beneath her feet was still stained with white splatters from the geth they had destroyed. The corpses were gone but for a few abandoned bits and pieces, perhaps taken by the council's researchers. Above and around them writhed the gnarled roots of overgrown vegetation, left untouched for fifty thousand years.

"This place gives me the creeps," she shuddered.

Garrus smirked at her, but the expression seemed forced. "You mean the dead protheans, the dead geth, or the dead VI that spied on us last time we were here?"

Shepard couldn't help but laugh, the sound echoing hauntingly in the great room. "All of the above," she said, and then silence reigned once more.

They powered up the complex and found the control panel, relieved to head back out into the sunshine when their task was done.

O'Connor flew them into the bunker. The three friends, waiting impatiently in the shuttle's hold, tried to forget that they were surrounded by the corpses of the last living protheans.

"I miss the Mako," Shepard commented with a sigh, remembering the last time they had made this trip. Garrus and Liara shared a look. "Hey, my driving wasn't that bad!"

Garrus gave her the turian equivalent of a snort. "The crew practically threw a party when we discovered that the Hammerhead wasn't salvageable after the Collector base crash."

"You're lying."

"Wish I was," the turian drawled, giving Shepard a mournful look. She rolled her eyes.

When they stepped out of the shuttle into Vigil's alcove, they found it shut down and powerless, just as the council had said. "It looks untouched," Garrus said, his voice echoing in the chamber. "I find it hard to believe that the Council didn't try to salvage anything from it."

Liara hummed thoughtfully. "I was never permitted in this part of the complex during the council's investigation. It was all very secretive."

Shepard scowled. "I half wonder if they didn't shut it down themselves, just to hide any evidence of the reapers." She walked up to the VI's hardware, eyeing it. "Whatever they did, we need to figure out how to extract the core. EDI thought that would be the best way to study it."

Garrus linked EDI into his visor feed, taking a closer look. "What do you think, EDI?"

After some direction from the AI to examine various parts of the hardware, she concluded, "It appears to be possible without further damage of the hardware. I will guide you through the process."

Shepard slapped the turian on the shoulder before taking a few steps back. "Well, Garrus, looks like you're up." She held no illusions about her lack of technical skill.

With EDI's help and Shepard's oversight, Garrus and Liara managed to detach Vigil from the mainframe of the prothean bunker, hauling the VI's hardware onto the shuttle. As O'Connor left to cart Vigil to the Normandy, Shepard turned to Liara.

"Alright, prothean expert, what's our next step?"

"We need to head towards the research labs," Liara said, pulling up the map. "I believe they are located in this area of the complex." She marked a location on the map.

"I hope the council left something for us to find," Shepard remarked.

Liara shook her head. "In truth, I feel the council's visit here was less of an information gathering mission and more of an attempt at press relations. I do not think they made any great effort to acquire information in fear that it would corroborate the idea of the reapers. They have spent the last several years trying to silence the truth."

Shepard clenched her teeth and headed in the direction Liara had marked on the map. Once she had created a little distance between her team and herself, she allowed herself to mutter obscenities under her breath in her anger.

The three of them continued down shadowed, twisting hallways and angled elevators, none of them entirely sure what might lay ahead. Turning a sharp corner, Shepard paused at the sight of bright light at the distant end of the corridor. "We're too far underground for that to be sunlight," Shepard stated. It didn't look anything like the soft glow of the prothean lights that remained in the ruin.

Liara seemed at a loss. "That is not possible," she insisted. "There has not been an expedition here in well over a Citadel standard year. The council restricts travel to Ilos tightly."

"How certain are you?" Shepard asked.

Liara paced across the narrow width of the corridor, obviously agitated. "I researched this thoroughly, Shepard," she maintained. "If anyone is down there…" She trailed off, turning to the commander with a worried look in her eye. "They must have significant resources and nefarious intentions."

Shepard nodded in agreement. "Weapons out," she instructed, "But don't fire unless necessary. We don't know who they are or why they're here yet."

The three of them made their way silently down the corridor and turned the corner to see an open door to a laboratory—and two human scientists within.

The female scientist—the obvious leader—pulled a pistol from her hip holster almost as an automatic reaction. She faced down Shepard and team, weapons out but none of them moving.

"See, Ashar?" she called over her shoulder to the cowering scientist in the corner behind her. "I told you to never leave home without your pistol." She paused, fixing Shepard with a hard look and tightening her grip on the gun. "Even on Ilos."

Silence reigned for a long moment as the two parties appraised each other. "Who are you and why are you here?" the scientist demanded.

Shepard quirked a brow. "I think I'll be asking the questions, thanks." In her peripheral vision she saw Liara glowing with biotics and Garrus with his rifle trained on the scientist's head.

"Oh, really?" she protested. "And why's that?"

Shepard holstered her gun and smirked at the scientist. "Because that pistol will hardly graze my barrier," she told her. "And because I'm a Spectre."

The scientist had an incredulous look. "Commander Shepard?" she questioned, unable to hide the surprise in her voice.

"So you've heard of me," Shepard deadpanned, crossing her arms over her chest. "I suggest you start talking. You might want to begin with your name."

With some hesitation, she holstered her pistol. "I'm Doctor Felicia Arbaugh, and this is my assistant, Doctor Ashar Prentix," she said, jerking a thumb behind her to the still-cowering man at the back of the lab. "And we're researchers," she added. "Obviously."

Shepard chose to ignore the woman's attitude. "Researching what?"

Doctor Arbaugh crossed her arms loosely, mimicking the commander's stance. "The Protheans."

"I want specifics," Shepard demanded. "And I'm not feeling patient."

Arbaugh shrugged. "It will be easier to show you." She motioned them forward but eyed them before she moved. "Assuming you won't shoot me the moment my back is turned."

Garrus let out a threatening growl, but Shepard held up a hand to stop him. "If I wanted you dead, we wouldn't still be talking," she told the scientist matter-of-factly. "We won't attack without reason."

The scientist's eyes narrowed, but she turned and strode to the back of the lab, the skittish Doctor Prentix moving out of her way. She moved purposefully towards a lumpy table covered in a white sheet. With a glance at her audience, Arbaugh yanked the sheet away to reveal something that shocked all three of them.

"Goddess," she heard Liara breathe from beside her. "Is that a Prothean?"

Shepard stared at the body, unable to tear her eyes away. Its similarities to the Collectors were undeniable, and—her breathing hitched—

The smell of burning flesh and sound of screams assaulted her senses. The voice, full of fear, spoke of untold destruction. His warning was cut off as he cried out in pain, the same pain wracking her body. She felt his moment of terror and regret. Too late, he thought. Too late.

"Commander?" The dual toned voice, laced with concern, snapped her out of it.

Shepard ripped her eyes away from the dead prothean and back to the scientist. "What are you doing with her?" she demanded coldly.

The scientist still faced away from them as she spoke. "The seals still held on some of the cryo pods," she explained emotionlessly. "They might be dead, but then again, so were you."

Shepard stared at Doctor Arbaugh's back, and a dangerous sort of calm flooded her. "Why?" she asked flatly. "Why bring them back?"

"To fight the reapers, of course," Arbaugh said scornfully. But then her voice turned almost gleeful. "What if you had an army of the best soldiers and scientists at your command? To follow your every whim? To fight and die for you?"

Shepard felt the unease of her companions on either side, but her focus was entirely on the scientist. "You want to control them," she stated, taking a few steps forward towards the table. "You want to make them fight a war for you, one they've already died for." Her voice was dangerously low. "That's sickening."

"Is it really worse than the things you've done, Commander?" Arbaugh challenged. "A whole system gone," she mused falsely. "They were just batarians, of course, but still."

Shepard tried to suppress her fury. "I only did what was necessary."

"So did I," said the scientist, and suddenly she whipped around, faster than anyone could react, and pressed her pistol to the commander's head. Shepard felt a wave of self-reproach for being too distracted to stop her. At point-blank range, her shields were useless.

"You have a death wish, Arbaugh?" she questioned through gritted teeth. "You can't expect to survive this."

The scientist let out a cold laugh. "I know you, Commander, and I'd rather die than go into custody," she said, and her eyes glinted. "At least this way I can take you with me."

Before the scientist could attempt to pull the trigger, Doctor Arbaugh went rigid, the blue glint of a biotic field shimmering over her body. "No, you can't," Shepard countered. She held the stasis field steady as she pried the pistol out of the scientist's hands.

"Who do you work for?" Shepard demanded tersely. She loosened the stasis just enough for Arbaugh to answer.

With a cold glint in her eye, the scientist said, "Cerberus."

A sharp sound rang out, a bullet slamming through the scientist's head at point-blank range. Arbaugh collapsed to the floor atop a puddle of her own blood, already dead. Silence fell.

All three of them turned from the dead scientist at the sound of a whimper. The assistant, Doctor Prentix, ran for the door. He was fast, but Garrus was faster. "What do you want to do with this one?" he asked, voice full of disgust at the human trying to writhe from his grasp.

Still feeling numb, Shepard spared the assistant a cold glance. "Tie him up," she ordered, and turned to Liara. "Once we're out of here, contact the Alliance anonymously. Let them know we've got a Cerberus scientist trussed up for them to interrogate." The scientist let out another whimper, but it was ignored.

The commander looked around the room. "Looks like the rest of the Prothean labs are through the door. Gather any data you can, wipe everything, and let's get the hell out of here."

The Prothean lab was devoid of power, like Vigil, but they took the memory cores of each computer for later analysis. The Cerberus scientists' data, on computers powered by portable generators, was downloaded and wiped from the memory.

Shepard smashed the remainders of the Cerberus equipment, leaving the team in near darkness, and turned to the dead Prothean laid out on the table. She didn't have time to put her to rest, nor did she know anything about Prothean funerary rites. But she pulled the sheet over her gently and carefully, covering her body once more.

She took a deep breath and turned back to her team. "Let's go," she said. They trudged back to the landing zone and boarded the shuttle in silence.

"Transmission for you from EDI," the pilot told her, and Shepard activated her comm, frowning as she listened. EDI's news would have come as a blow if she hadn't already felt so numb. As it was she barely reacted.

"Thank you, EDI," she said tiredly, once the AI finished speaking. She glanced first at Garrus and then Liara, both looking at her questioningly. She let out a sigh, but her voice betrayed no emotion. "I'm now officially a fugitive from the law. As is anyone traveling with me."

Somehow knowing this was coming did nothing to prevent the shock Shepard read on both their faces. Unable to deal with it, Shepard turned away.

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