Running Silent:

Commander Undercover

…

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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Several weeks had passed since Shepard first set the ex-Cerberus scientists the task of subverting a mass relay, and Shepard had filled those weeks with a variety of missions, mostly intel-gathering to support the scientists. Every scrap of information that could be found on the mass relays was collected and analyzed, and the scientists seemed to think they'd made a good start of it. What they needed was time to work, and that was the one thing Shepard couldn't give them. The day was soon coming when the reapers would reach the Kite's Nest relay, and then their time would be up.

She collected more scientists, corresponded with members of her crew that were away, and helped her friends prepare their people for the coming invasion. They all knew the time would be coming soon, but if the scientists couldn't stop this, well…

She didn't have a plan B.

…

"Primarch, sir," Garrus greeted, raising his hand in a salute as the turian's image appeared in the Normandy QEC.

"At ease, Vakarian," Fedorian waved him off. "I'd like to hear about your progress."

Garrus dropped his hand and attempted, unsuccessfully, to relax his stance. He was still speaking to the primarch, after all. "As you know," he began, "My men have been traveling to our major military installations and doing inspections. Most passed our specifications, but the report is on your desk for those that didn't," he told him. "Early warning beacons have been placed throughout Hierarchy space that will detect and report enemy movement." Garrus didn't bother telling him that they would be more likely to detect the reapers by being suddenly cut off from the beacons. It would be obvious enough when the time came.

"I've got my scientists working on developing a weapon that works well on reaper troops. They have my reports and vids on husks, and believe that they can develop a weapon that could interrupt the nanides that control the creatures," he explained.

"And will these weapons translate to other applications?" the primarch questioned.

"I'll find out," Garrus promised, knowing full well that Fedorian wasn't completely sold on the reaper threat.

The primarch gave a sharp nod. "I've received your proposals for supply line and evacuation security protocols. Extreme but effective," he complimented grudgingly. "And I have your analysis of our defenses," Fedorian added, giving the other turian a steady look.

"Sovereign cut straight through Citadel defenses," Garrus reminded him. "Security may be stronger than it was three years ago, but the best we're going to be able to do at this rate is slow them down."

"Hmm," was the only response Garrus received. The primarch changed the subject. "I also received your request," Fedorian told him, raising a browplate.

Garrus thought this one might be a problem, and he'd been prepared to argue for it. "The cost may be high, but this will be well worth it, sir," he said preemptively. "The comm buoys are easy targets, ones that any enemy would exploit immediately, leaving us directionless and disorganized. A quantum entanglement device on each colony or major military base may be the only way we can keep up consistent communications throughout Hierarchy space. Without comms our military will be about as useful as wings on a xemna." Garrus closed his mouth abruptly. He had to stop himself before he got too heated.

The primarch let out a heavy sigh. "Vakarian, do you have any understanding of how expensive this venture would be? It was a great undertaking to install the few we have," Fedorian reminded him.

Garrus looked the primarch levelly in the eye. "I'm aware of the cost, sir, but I believe it will become necessary."

"I'll consider the request, Vakarian," he said, closing the subject. "There is another reason I called. I have a mission for your squad, one of high urgency and absolute secrecy."

Garrus straightened subconsciously, putting his hands behind his back. "Sir?"

"Vakarian, are you familiar with Axion?"

Garrus wracked his brain but couldn't find the connection the primarch was looking for. "No, sir."

"It's the Hierarchy's biggest black op," the primarch stated. "And it's gone dark." He began pacing. "Axion is a research lab, tasked with studying alien technology of all kinds."

Garrus's mandibles flared at the realization. Reaper tech. It was always reaper tech.

Fedorian studied his expression. "I trust you know where this is going," he said dryly. "The Axion lab studied remnants from the battle of the Citadel. This is the lab that developed the Thanix cannon. Due to the Sovereign connection, I felt your team was the best suited for this task. Take a team to find out what happened there. Contain the situation and report back. I doubt I need to tell you that this is a matter of the utmost secrecy."

"I understand, sir," Garrus responded quickly. "Is there anything else you can tell me about the lab?" he asked, mind already racing with possibilities and plans.

"I'll send you a written briefing through a secure channel. Dismissed." The primarch's image faded, leaving Garrus alone to consider the enormity of the situation.

How many turians had lived and worked and studied under the shadow of a dead reaper? Garrus remembered his own experience with a reaper corpse, and shuddered.

…

Joker watched from the mess hall as the lone female turian on the ship wandered into the main battery and back out moments later. "Sup?" he called as she came back down the hallway.

"Have you seen my brother?" she asked, glancing first at Joker and then at a couple of crewmen sitting a few seats down.

"I think he's in a meeting with Shepard," Hawthorne helpfully supplied.

Joker barked out a laugh. "A meeting. Right." He rolled his eyes. "I'm sure they have lots of things to 'discuss' alone together in her quarters." His eyes darted over to Solana Vakarian standing at the end of the table looking mildly disgusted. "Oh, shit, I didn't just give away the big secret, did I?"

"No," came a voice from the hallway. "Garrus told Solana about us before she came onboard." Shepard appeared from the shadows, arms crossed and look of mixed amusement and annoyance on her face.

"What?" Joker protested. "She finds out before she even gets on the ship, and you didn't even tell us? No fair!"

She snorted. "Did you expect me to get up in front of the ship and make an announcement? Besides, Solana is family. She gets precedence. It wouldn't be right for her to find out from your terrible innuendo," she teased. "By the way, it was a real meeting. Miranda was there and everything."

His grin widened. "Miranda? Niiice."

"Joker," she warned, but the corners of her lips quirked slightly. He held in a grin. She always pretended his jokes weren't funny, but he knew better.

"Solana," she directed to the turian, "We've got a new mission. I want to see you in the briefing room in half an hour." With that, she disappeared back into the hallway, leaving Joker and Solana staring at each other.

"Do you always talk about the commander's sex life that way?"

Joker smirked. "Please. I talk about everyone's sex life that way."

Her look of disgust was obvious even to a human as she hurriedly disappeared towards the elevator.

…

Garrus was nervous as the team slowly filtered into the room.

He hadn't run an operation like this since his team on Omega. Actually, he considered, thinking of what they expected to face, he'd never run an op quite like this.

The Migrant Fleet had been a diplomatic mission. Palaven had been tactical. And on Omega he'd never had to deal with reaper artifacts and indoctrination.

Those were par for the course when it came to missions with Shepard, but this time he was in charge and it wasn't husks that they feared—it was something different.

"They've been studying reaper technology there for how long?" Miranda questioned. Her face was expressionless, but the tension in her voice was easy to read.

"Since the battle of the Citadel," Garrus answered. "They have pieces of Sovereign."

Shepard shifted uncomfortably in her seat. "Then there's something we need to consider. We may not simply be facing a case of indoctrination."

Garrus stared at her. "What do you mean?"

Her expression was solid, her voice falsely smooth. "We know what reapers eventually do with humans they indoctrinate. I can't see why they wouldn't try something similar with turians."

Miranda was visibly repulsed for a moment before she schooled her expression. "Are you saying there's a chance we'll find turian husks at this base?" she asked carefully.

Shepard looked grim. "That's exactly what I'm saying."

Garrus tried not to shudder at the memory of her words. He would have no hesitation in shooting to kill, but the idea of facing down husks created of his own people was not a welcome thought.

Zaeed was the last to enter the conference room, walking in with a swagger and full set of armor, as usual. "Looks like we're all here," he said casually. "So let's get a bloody move on, eh?"

Garrus glanced aside to see the skin around Shepard's eyes tighten slightly, but she didn't rise to Zaeed's bait. "Alright, people, listen up," she called. Attentive eyes fell on her from around the room. "Deputy Commander Vakarian is taking the lead on this mission. I expect each of you to follow his orders without question," she said carefully. "As I am currently a fugitive from the law, I'll be undercover. Anyone who breaks my cover by questioning his orders or so much as glancing at me for secondary approval will be scrubbing the head with a toothbrush. Understood?"

At a chorus of "Yes, ma'am," Shepard relaxed slightly and turned to give Garrus a nod.

He cleared his throat. "A turian lab studying reaper tech has gone dark," he explained. "We've been tasked to investigate and report back." He typed a command on his omni-tool, and pulled up a schematic of the building in the center of the table. "A couple of my Hierarchy operatives will be scouting out and meeting us when we arrive. We will split into teams to utilize both points of entry for the bunker and systematically make our way through to meet in the central lab," he explained. He crossed his arms, settling back on his hip to look at the team. "The central lab almost certainly holds wreckage from the battle of the Citadel."

There were a few worried looks and discontented murmurs throughout the room, but under his gaze they quickly returned to focus.

"As both teams make their way through the lab, we'll be downloading any data possible from the lab computers and placing explosive charges at specific points marked on your maps. The largest of these charges will be placed in the central chamber. Our primary objective is the destruction of that base. We can't allow any reaper tech to survive." It wasn't what the primarch had requested, but Garrus understood better what needed to be done.

Garrus took a deep breath. "This lab has been studying reaper tech for over two years, which means that everyone inside must be assumed indoctrinated." He gazed around the room to meet the eyes of each teammate. "No one can be allowed to leave that bunker alive. The risk is too great." Garrus studied their reactions, knowing that Shepard and Miranda were doing the same. Anyone that balked at this stipulation had to be left behind.

"We all know what the reapers are capable of, so be prepared for anything when we enter that lab," Garrus stressed. "You'll receive your assignments by the end of the day. See me if you have questions or concerns. Dismissed."

Garrus stared down at the conference table as the team filed out quietly, leaving no one in the room but himself and Shepard. He wondered if he should have warned them about the possibility of turian husks. He hoped that his vague warning would be enough, but he wasn't certain. There were too many things that weren't certain about this mission. He was used to going into things blind while Shepard was leading, but every one of his Archangel operations had been carefully planned and executed down to the last detail.

If he couldn't save his team then, how could he expect to safely lead Shepard's now?

A small human hand wrapped around his forearm, and he looked into a pair of smiling blue eyes. "You're doing great," Shepard told him. He studied her expression. Did she mean it or was she simply trying to bolster his confidence?

She raised a knowing brow at him and leaned against the table. "You know, Vakarian," she began, sounding just a hint exasperated, "If you think I'd let you lead my team into danger without being sure of your abilities, you don't know me at all." She gazed at him loftily, a challenge in her eyes.

His browplates lowered slightly as he regarded her. "You take chances on people all the time."

"No I don't," she countered, the corners of her lips turning up into a smile. "I just give people the opportunity to prove what I already know."

She levered herself off the table and gave him a small smile before turning and walking out of the room to leave him with his thoughts.

…

Commander Shepard was not a woman who put much thought into clothing.

She wore uniforms, fatigues, and armor. There was that one time with Kasumi and the dress, but everyone knew better than to speak of that lest they be eviscerated.

It was true that she could spend hours on her armor, considering which pieces were best suited and what upgrades could be added, but never before in her life had she been forced to choose her armor based on looks.

"My N7 armor is too distinctive," she explained to the girls on her couch. "I can't be recognized."

Tali, Kasumi, and Solana nodded along, but Shepard suspected they were only here to observe and make smart comments, considering that they'd brought alcohol and made no attempt to be helpful as of yet. Tali always seemed to materialize when clothes were involved, living vicariously through her non-quarian friends, and Kasumi literally materialized fairly often, usually when an opportunity to tease her commander presented itself. Solana had been dragged here by Kasumi. Shepard still hadn't decided if their friendship was a good thing.

"Cerberus stocked my closet with a bunch of armor that I always ignored, so I figured I could pick something out of what the Illusive Man left me." Shepard turned back to the wardrobe and pulled open a drawer, tugging out a pristine set of silver armor with odd shapes and red accents, and what appeared to be a dragon painted on the chest. Shepard thought it looked stupid, but she wasn't the fashion expert in the room. She looked down at the armor and over to the other women. "Thoughts?"

Tali cocked her helmet to the side, letting her straw slip out of its port. "Why are the shoulders shaped so funny?"

Kasumi made a humming sound. "It looks like they were trying to imitate an ancient Earth style from the stories," she said. "Knights in shining armor killing dragons for princesses… that kind of thing." She smiled under her hood.

Shepard laughed. "You read too many fairy tales, Kasumi." She looked at it speculatively. "I think it looks a bit like turian plates." This made Solana snort, so Shepard placed the armor back in its drawer without further comment. Anyways, she was supposed to be undercover, not sticking out like a sore thumb. She opened the drawer below it, pulling out a set of white and yellow armor she already knew was going to be a bust.

"I can't believe the Illusive Man thought I would wear this," she said with a roll of her eyes. The Cerberus logo was embarrassingly prominent. "Who wants to help me toss this one out the airlock?"

"I do not believe that would be wise, Commander," EDI interjected.

Shepard blinked. "EDI? You've been watching?"

"I am always watching, Commander. It has been edifying," she said. Very creepy.

Shepard put a hand on her hip and looked up towards the comm unit. "So why shouldn't I space it? Please don't tell me you've still got some loyalty to Cerberus locked up inside those great big processors of yours."

Tali giggled. "Mmm, big processors…"

Shepard rolled her eyes. The quarian never could handle her alcohol.

"I believe the armor will be useful in case of infiltration," EDI explained. "Since we are currently encountering hostile Cerberus forces an estimate of once per solar week, I believe such measures may be necessary."

"Good idea, EDI," Shepard said. "Guess I'll have to hold onto this crap."

She put the armor away and went for the last drawer, hoping that it wasn't something bad enough to stick her in that weird dragon armor. What she pulled out was black and red and rather intimidating. She smiled to herself and turned towards the couch. "I think this is it, guys."

Tali took a long sip of her drink. "I don't know," she considered. "I don't think it will be very flattering on you."

"Seriously?" Shepard gave her friend a look of disbelief. "Your biggest concern is how attractive I'll look in the armor?"

"Oh, I don't know," Kasumi said slyly. "I've noticed a certain turian checking you out on the battlefield."

"Garrus always watches my back," she replied impatiently. "It has nothing to do with that."

Tali let out a high giggle. "I'm sure he loves watching your back…side." Consumed by laughter, she fell sideways onto Kasumi's lap.

Solana looked at them in disgust, letting out a quiet, "Ew."

Shepard let out an exasperated sigh. "Jesus, it's like living with a bunch of children."

EDI chimed in. "Tali is correct, Shepard. Your current armor choice will significantly diminish your visible waist-to-hip ratio, one of the foremost aspects of turian attraction."

Shepard groaned while her friends stifled laughter. "You too, EDI?"

"I am simply offering analysis and advice," the AI said, an obvious note of humor in her voice. "If you do not wish for my suggestions in regards to your love life, I can retain a respectful silence."

Shepard heaved a sigh, dropping her face into a hand. "Yeah, EDI, I think that might be wise."

…

A/N: Thank you for making it this far! I know it's been a long road with no reapers as of yet, but that's going to be changing very soon. ;)