Running Silent:

Divided Loyalties

…

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.

…

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.

…

Shepard felt a distinct surge of satisfaction when the doors opened into the war room. Data feeds were running, muted news vids were displayed on screens on the walls, and crew worked the consoles, receiving and filtering incoming information.

Her eyes fell upon her new intel officer. "T'Nara," she greeted. Hestia lifted her eyes from the center console. "I hear you have something for me."

"Several things for you," she corrected, as serious as ever. "You may not be able to act upon all of them."

Shepard rested her hip against the console and crossed her arms. "I'm listening."

Hestia gave her a short, businesslike nod. "As per Doctor T'Soni's instructions, we've been searching for any sign of reaper artifacts. Secret research programs, unusual archeological digs, that kind of thing," she explained. "We know that each council species has a number of pieces of Sovereign under study, but these are all government protected programs and difficult to pinpoint. We did find the location of one that was not, however."

"Sounds good," Shepard affirmed. "Who is it and where?" She fixed her eyes upon the asari.

"Cerberus, unsurprisingly," Hestia told her, without even the smallest hint of irony. Why couldn't Shepard ever meet an asari that had a sense of humor? "It's an outpost in the Caleston Rift. Cerberus is the only organization seen coming or going from the planet."

"An uncharted world," Shepard mused. "Sounds like fun. Wish we still had the Mako."

Hestia's expression leaned towards a disapproving frown, but she didn't comment.

Shepard straightened up and gave her officer a nod. "Send a briefing to my private quarters. I'll take a closer look."

"It will be on your terminal by the time you arrive," Hestia affirmed.

"Efficient, T'Nara," Shepard praised her. "I think you're going to be a good addition to the crew."

Before turning away, Shepard thought she might have actually seen a smile grace the asari's features.

…

Garrus felt his mandibles relax into an involuntary smile the moment Jane Shepard's face appeared on his omni-tool vidscreen. "Hey, Shepard," he greeted. "I didn't wake you did I?"

She was adorable in messy hair and pajamas, the glow of her omni-tool lighting her against the backdrop of her darkened cabin. "Nah," she dismissed and gave him that particular smile he loved, the true one that was more precious to him than all the stars in the sky. "I wasn't going to go to bed without hearing from you. Solana wanted me to let you know that your mom's settled in at the Helos facility, by the way."

"Thanks for letting me know. How do you think Solana's doing?"

Shepard shrugged. "Mostly fine. She seems a bit lonely right now with you gone—especially since Kasumi had taken her under her wing. I can't decide if that's a good or bad thing." She grinned. "How's it going over there?"

"I met with Admiral Koris today and we discussed our options," he told her. "We didn't decide anything for sure, but no matter what we do, it's going to cause a stir."

"Tell me what you're thinking," Shepard requested, resting her chin on her hand thoughtfully.

"Well, Kasumi did some recon and found out that there's more dissent about this war than we thought. No one realizes how widespread it is."

"That's good," Shepard said. "You can use that."

"Yeah," Garrus replied. "We're going to try to get the dissenters connected and organized. There are a lot of captains among them."

"Even better," she added, smiling at him reassuringly. "That's a good start. What about the admirals?"

Garrus let out a low hum. "You know where Koris stands. Raan is playing peacekeeper and Xen just wants to experiment," he said, unable to hide the thrum of disgust in his voice. "Gerrel is as war-mongering as ever, and the new admiral, Jorah, is of a similar mind, or so Tali tells me," he explained.

"Are you going to meet with them?" she asked, and Garrus hesitated.

"Maybe," was his answer. "We have another plan. It's… dramatic, to say the least. But it might be our best shot."

"Tell me," Shepard instructed, her intense eyes meeting his even across the vid connection.

Garrus took a deep breath. "Shepard, are you still in contact with Legion?"

Shock registered on her features before she reigned herself in. "I am," she said cautiously. "What are you getting at?" She leaned forward slightly, her body language betraying the calm she projected.

"I've asked for a meeting with the admiralty board, and I'm hoping you might be able to get me a vid of Legion explaining that the geth aren't interested in war with the quarians."

Shepard frowned slightly and looked like she wanted to speak, but Garrus precluded her. "We can blackmail them with it, if necessary. Threaten to broadcast the vid across the Flotilla if they don't see reason." His mandibles fluttered slightly as he waited for Shepard's reaction.

A slow smile bloomed on her face. "I think I can give you better than that, Garrus," she said. "I think Legion would consent to a live feed."

The wheels were already turning in his head. "He could talk to them and answer questions. If they still want to cause trouble, I could record the meeting and threaten to release the vid. That would be even more damning."

"You know that this could all backfire, right?" Shepard asked, raising a curved brow at him. "This is the last thing they're going to want to hear."

"I know," Garrus agreed. "But I have to try it." He was going to do whatever he had to—he wouldn't fail Shepard or Tali on this.

Shepard's eyes sparkled. "I like it. Garrus Vakarian, all grown up and causing trouble," she teased.

"I was Archangel," he reminded her smugly, his mandibles flaring into a brief grin.

He thought he saw her face freeze for a split second, but it could have been the connection.

"I'll contact Legion," she told him. "You keep doing what you're doing, big guy. I'm proud of you."

The call ended, and Garrus smiled to himself. He could do this.

…

"Kal!" Tali waved at the red-suited quarian when she saw his figure across the room. "I haven't seen you for a few days."

His approach was strangely slow. "You seemed busy, ma'am," he said hesitantly. "I didn't want to bother you." He glanced to her left, and Tali suddenly remembered that she wasn't alone.

"Kal, this is Garrus Vakarian. You might not remember, but he was one of Shepard's team that got us off Haestrom," she reminded him. "Garrus, you remember Kal'Reegar," she added, and felt her face flush. Keelah, she was glad of the helmet sometimes!

Garrus inclined his head towards Kal'Reegar. "Nice to see you again, Reegar. I'm glad your injuries have healed." It was odd, Tali thought, but her friend's voice sounded a bit stiff. She wondered why. He knew how much she liked Kal.

Kal'Reegar stood up straighter than before, if that was possible. "Vakarian," he greeted. "Are you here to visit Tali'Zorah?"

There was a strange sort of tension in the air, Tali realized, but she didn't know what to make of it.

Garrus shifted uncomfortably, probably uncertain of how much he could share with Kal. Tali hadn't told him how much of their situation she'd discussed with the other quarian. She had no desire to be teased about Kal more than she already had.

"Diplomatic mission, actually," he said. "Though I'm hoping Tali will be able to return to the Normandy with me afterwards."

Something changed in Kal's stance, but he didn't give Tali the time to study it. "I see," was all he said. "I better get going," he told them, and gave them each a nod. "Vakarian. Ma'am." And he disappeared down a hallway.

Tali and Garrus walked on quietly, Tali puzzling over Kal's sudden change in demeanor. She thought he was upset or bothered by something, but she wasn't sure what. A fluttering hope within her thought that maybe he was unhappy she might be leaving soon.

…

"I don't think this is a good idea, Shepard."

It was an odd day when Shepard was more composed than her XO. Miranda's usually calm demeanor had disappeared, leaving something oddly agitated in its wake. Shepard wasn't quite sure what to make of it, but she couldn't let it delay the mission.

"If they have reaper tech, we need to deal with it," Shepard countered patiently. "We can't have indoctrinated agents running around. I know it's a risk, but it's one we should take." There was something desperate in the brunette's eyes, but Shepard didn't have time to work it out, not when they were hitting atmo in half an hour.

"It's a Cerberus outpost," Miranda argued. "They'll probably have some kind of alert set up. They'll come after the ship while you're groundside."

Shepard raised a brow at her XO. "Then we'll have to take care of the situation quickly, won't we?" She crossed her arms. "My team can take care of ourselves, Miranda. If the Normandy has to make a quick getaway, we'll be fine. We'll keep the shuttle on the ground just in case."

Miranda, rarely one to initiate a touch of any kind, placed her hand on Shepard's arm. "I really don't think you should do this," she said quietly.

Shepard hadn't decided yet how to respond to the disconcerting action before they were interrupted by EDI's voice. "Commander, you have a call from Liara coming in over the QEC."

"I better take that," Shepard told Miranda. "Don't worry," she added. "Everything will be fine."

Shepard made her way to the QEC to see Liara's hologram looking worried. What's with everyone today? she wondered.

"What's going on, Liara?" she asked brusquely. "I'm short on time." She was mentally working out whether she'd be late getting ready for the mission. Commander Shepard didn't do late.

"We need to talk about Miranda," the asari told her, looking more like the old, scared Liara than the one she knew now.

"Miranda?" Shepard repeated. She let out an annoyed sigh. She didn't have time for this. "Can it wait until after the mission?" she asked, her voice revealing more frustration than she meant to. "I have to meet the team at the shuttle in a few minutes."

EDI helpfully piped up, "Eight minutes and forty seconds, Commander."

Liara was silent for a moment, expression unreadable. "I—" She paused. "Very well, Shepard. We'll talk after the mission," she conceded. "But please," she added, "Be careful."

"Aren't I always?" Shepard told her with a grin. Liara didn't smile back.

The hologram faded and Shepard stepped out of the room, headed for the elevator. "EDI," she addressed, "Are Zaeed and Solana down at the shuttle?"

"They are in the cargo bay gathering their weapons," the AI answered.

Shepard got into the elevator, pressing the button. "Thanks," she replied. As she waited for the elevator to descent, her brow creased slightly. What the hell was going on with Miranda? Something had gotten her spooked, probably something to do with Cerberus based on the XO's reaction to this mission. Liara knew something, but Shepard would rather get it out of Miranda first, if she could. In either case, it would have to be dealt with after the mission.

She walked out of the elevator into the shuttle bay with her usual confident stride. "Ready to raid a Cerberus base?" she asked her two teammates, and grinned.

…

Shepard was in a strangely good mood when the shuttle landed outside the prefab unit. Solana shot her a questioning look.

"Back on the SR-1 we took out a bunch of these outposts," Shepard told her. "Seems like we stumbled upon one at least once a week." A faint smile crossed the commander's face. "Reminds me of the old days."

Solana decided that Shepard really was a very strange human.

The commander stepped aside when they reached the locked door of the outpost, motioning Solana forward. Garrus had warned her that technical comprehension was one of the commander's greatest failings, perhaps only behind her driving skills. Solana hadn't actually seen either of those 'skills' in action yet, but she knew to expect to be called upon for hacking duty.

Solana had been encrypting and hacking doors since she was tall enough to reach the lock. It was a game she and Garrus had played for years—he would find a new and creative way to lock his bedroom door, and she would find a new and creative way to unlock it. Her parents had studiously ignored their game, perhaps understanding the real-world practice such games would give them. Given how many times Solana had broken into her father's study and personal terminal, maybe they should have paid more attention.

The light on the door blinked from orange to green, and Solana stepped back so that Shepard could take point once again. The panels of the door split apart to reveal an empty room. "Keep your guard up," the commander warned. She confirmed the room was clear, then led Solana and Zaeed down a narrow hallway. With a short glance back at them, she hit the switch to open the door at the far end.

The panels parted to reveal a room swamped with supply crates, blocking much of the room from view. Solana did see something odd, however. "Commander?" she began to question, but Shepard seemed to notice the objects at the back of the room just as she did.

The commander's eyes locked onto a series of tall metallic spikes lined up along the back wall. Something dark and oddly shaped seemed to be impaled upon them. As if somehow alerted to their presence, the spires began to collapse into themselves before the strange, glowing masses started to move.

"Shit," Shepard swore, and pulled her pistol out of the holster, her other hand already beginning to glow with biotic power. "Maybe a bit too much like the old days," she muttered.

Within moments, Shepard and Zaeed had jumped into action, but Solana was still staring. Spirits, those things were moving. They were alive… and looked almost human. They were climbing off the collapsed spikes and running directly towards the squad.

"Don't let them get within melee range!" Shepard barked.

She snapped out of it and started shooting. A few bursts from her rifle took each one down, but there were so many. A door at the back opened and more of those creatures began to pour out. Shepard was lifting, slamming, and knocking them off their feet, and Solana tried to keep up, shooting down each one before it could rise again.

One broke through and ran right up to Shepard. With a biotic burst she threw it off her, and Zaeed put a few rounds through its skull. "I hate husks," Shepard huffed, tossing out a shockwave.

Husks. Somewhere in the back of Solana's mind it registered; these had been part of the stories Garrus had told, the ones she only half believed. Solana dropped the last husk that had been running at her, and looked down to see the creature she'd killed—if 'kill' was even the right word. Revulsion filled her as she pictured the humans she had known, trying to find the link between them and these husks, a mockery of the people who they'd once been.

Had Garrus downplayed the disturbing nature of his adventures, or was he simply immune to the horrors after seeing so many?

Solana startled at the feeling of a hand on her arm. She found Shepard gazing at her with a look she couldn't quite decipher. Shepard held her gaze for a moment, but glanced behind her at a sound of annoyance.

"Bloody amateur," Zaeed muttered, and headed towards the back of the room, where the metal spires still stood.

Solana bristled at his words, but felt that hand on her arm give her a squeeze. "Don't mind Zaeed," Shepard told her. "His bark is worse than his bite."

Solana gave Shepard a blank look, and the commander's expression morphed into a small smile. "Human expression," she explained. "He's not nearly as much of an ass as he pretends to be."

"I heard that," the man in question called from the other side of the room. He crossed his arms, looking disgruntled. "Can we get a goddamn move on?"

Shepard took a step back, releasing Solana's arm. "Come on," she ordered. "We need to check out the back rooms." She turned on her heel, and Solana scrambled to follow, gun lowered but at the ready.

The room on the left was clearly the living quarters. Shepard ordered a quick sweep, but they found little of interest. Then they turned to the room opposite.

The doors opened to reveal a strange object in the center of the room, something Solana couldn't quite place as either machine or organic. It glowed with a blue like biotics, and had a presence that she could somehow feel in the room. "Spirits," she breathed. "What is that?"

Shepard glanced at her, mouth set in a thin line. "It's the reaper artifact they've been studying."

Solana's eyes widened, immediately snapping back to the object. She'd never seen anything like it. She took a step forward, almost subconsciously reaching out a hand—

An arm shot out in front of her. "You don't want to do that, princess." The mercenary stood beside her, looking at her with his one good eye. The other seemed to float lazily in her direction, clouded and unfocused. She pushed his arm away but didn't move towards the artifact again. Out of the corner of her eye she could see Zaeed still watching her.

Shepard made her way slowly around the reaper artifact, not looking at Solana as she spoke. "Has Garrus explained indoctrination to you?"

"A little," Solana answered, feeling way out of her depth. In her brother's stories none of this had seemed quite real. Standing in front of this reaper object, fighting husks and Cerberus and landing on planets that didn't even have names—it all felt a bit like some kind of dream that she was going to wake up from and find herself back in bed on Palaven. Garrus had said that this was big, bigger than anything she'd ever dealt with. She believed him, or thought she had, but she hadn't truly understood.

She thought she did now, though part of her still wished she didn't.

"Zaeed, Solana," Shepard called from the other side of the artifact. "We need to blow this thing up. Ideas?"

Solana gazed up at the pulsing object while Zaeed answered. "We could blow the power conduits," he suggested.

Shepard gave a small shake of her head. "Not sure the explosion would be big enough," she countered. "We need to be sure this thing is completely destroyed."

"What about a generator?" Solana asked. "They must have a big one."

Shepard seemed to consider for a moment, then nodded. "Find it."

Before they'd completed their task, a call came in from the Normandy. "Commander?" The pilot's voice sounded harried.

"What is it, Joker?" Shepard answered, brows lowering into a slight frown.

"Shit," he swore. "Cerberus knows we're here. I've got four fighters and a frigate inbound."

"Then get the hell out," Shepard ordered. "We'll get to the shuttle and meet you at a rendezvous point. Send O'Connor your coordinates once you're free and clear."

"Yes, ma'am."

Shepard turned to Solana and Zaeed. "Blow that generator quickly. We need to get to the shuttle ASAP."

Zaeed was the only one who seemed to take any satisfaction in the explosion. Shepard had become quiet and terse, focused solely on the mission. They headed for the shuttle as quickly as possible, and Shepard immediately headed for the cockpit to address the pilot.

"O'Connor, it's your chance to do some of that fancy flying you like to brag about," she said brusquely. "We need to get to the rendezvous point without being seen by any of the Cerberus ships in orbit."

Despite the situation, the shuttle pilot turned and grinned at her. "Don't worry, Commander," he said. "We'll be safe enough after we make the relay jump. Besides, I know some maneuvers. We'll lose 'em."

Shepard glowered at him. "Less bragging, more flying."

O'Connor cleared his throat. "Right. Lifting off now. You might want to strap yourselves in—this is going to be a bumpy ride."

…

Miranda strode onto the bridge, her body fraught with tension. "What's the situation?" she barked. Her fingers tightened into fists before she noticed and stretched them out again.

Joker's hands were flying across the console. "Cerberus. Four fighters and a frigate. Shepard told us to get the hell out, so I'm going to lose them and rendezvous with the shuttle in the Hekate system."

Miranda was silent for a split-second before making her decision. "No," she ordered. "We need to get to the Grenada system."

"What—why?" the pilot spluttered. "What's going on?"

"Damn it, Lieutenant, just do it! We need to hurry," she insisted. She hoped he couldn't hear the fear in her voice. "There's no time to explain."

Joker was silent for a long moment, obviously considering whether to listen to the XO or ignore her. He still didn't really trust her, even if Shepard did. Miranda's heart pounded in the silence.

"Okay," he said finally. "Sending coordinates to the shuttle."

Miranda felt a flood of relief, but one worry always replaced another. She left the cockpit, moving purposefully towards her next task. Her stomach churned. She'd made her decision. She just hoped that she wouldn't live to regret it.

…