Running Silent:

Aftermath

…

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.

…

The Normandy jumped from system to system in a path that Shepard hoped would be too long and complex for Harbinger to follow. She had given Joker the order to stop only after EDI assured them that Harbinger's odds of finding them were no greater than blind chance. The AI also took that opportunity to remind Shepard that the drive core was in immediate need of purging.

Shepard took their stop as an opportunity to have the crew reassess the damage to the Normandy, and she wound up less than pleased with what she found. The Normandy's first skirmish with Harbinger had not left her feeling confident about their chances. The hours during the purge and trip to the Citadel were so busy for her that she didn't even realize they'd arrived until EDI summoned her to the bridge. But the fact that she'd received such a summons, rather than the usual docking announcement, set off alarm bells in Shepard's mind. She dropped everything she was doing to rush to the cockpit.

"Joker?" Shepard said, a little breathless. "What's going on?"

When he spun his chair around, the expression on his face made Shepard's stomach drop into her boots. "We're grounded."

Shepard struggled against a sudden tide of mounting anger. "What do you mean, grounded?" She hadn't slept since before Menae, her ship was in need of serious repairs, and now the council was on her ass. This was the last thing she needed now.

"Council orders," Joker said. "Guess they heard about our relay stunt. They've 'requested' your presence." He added air quotes for emphasis. "Too bad Anderson isn't here to punch Udina out this time."

"I might punch him myself," Shepard muttered, glaring dangerously through the windows. She spun on her heel and marched out of the cockpit. If they wanted Commander Shepard, they'd get her.

Shepard was debating between two models of assault rifles when she heard footsteps behind her in the armory.

"This is your idea of preparing for a meeting?"

Shepard spared an unfazed glance Miranda's way as she strapped a rifle to her back.

Miranda grabbed her arm. "You can't march in there and wave your weapons around! They're already starting to think you're a loose cannon."

"Maybe I am," Shepard muttered, ripping away from Miranda's grasp.

"You're not," she said firmly. "And you need to prove it to them. Explain the situation. Use logical arguments to sway them to your side."

"Like that's ever worked before," she huffed. Shepard straightened and turned, finally meeting Miranda's eyes. "Are you offering your help?"

"If you'd like," the woman said evenly. "If not, I'll just offer two pieces of advice."

Shepard crossed her arms and looked at her expectantly.

Miranda looked her up and down, as coolly as ever. "Tone down that death glare a few notches," she said. "And you might want to consider brushing your hair."

The brunette turned and marched to the elevator, leaving Shepard staring after her, uncertain whether to be offended or laugh.

Before the elevator doors closed, Miranda shot her a small smile. "I'll be in my office if you want to talk. You can even borrow my hairbrush."

…

Shepard stormed back onto the Normandy in a worse mood than when she'd departed it.

"EDI," she called, marching through the CIC. "Is the primarch still aboard?"

"No. He and his entourage departed half an hour ago."

"Good," she said to herself. She entered the comm room. "Get me Liara on the QEC."

"Please," Shepard added as an afterthought. She ran an agitated hand through her hair, leaving no evidence of the care Miranda had put into styling it little more than an hour before.

"Commander, I must warn you that Garrus and Miranda are on the way to your location."

"Good," she snapped. "That means I only have to say this once."

The two officers burst into the room a moment later. "What happened?" Garrus asked. "Joker says we're still on lockdown."

Shepard's glare filled the room. "The council wants to debate and study the evidence. They'll call me back in two days." She paid no mind to the expressions of worry and shock on her officers' faces. "EDI, have you gotten Liara on the line yet?"

"Yes, Commander," she said. The asari's hologram faded into view.

"Shepard," she said, the name almost a sigh on her lips. "I am glad to see you in one piece. I heard about what happened."

"Then you must know about the lockdown," the commander said, brushing off her friend's concern. "I need you to find me a way around it."

Two sounds of surprise rang out behind her simultaneously. Liara stared at her with wide blue eyes. "Shepard, I—"

"That would be a mistake," Miranda said firmly. "Remember what I said before your meeting?"

Before Shepard could get a word out about Ilos, Garrus stepped in. "This isn't like before, with Saren," he said, as if reading her mind. "If we alienate the council, we're dead in the water. These alliances could fall apart, and you'll lose all the trust you've earned. That's not worth two extra days of freedom."

"I have to concur," Liara added hesitantly. "I don't think this will help in the long run."

Shepard stood among them, full to the brim with anger. She ached to fight, to do something. Now that she'd seen even a hint of the devastation being sown on the homeworlds, it was unbearable to think of sitting on her hands to wait for the council to decide her fate.

"You saw what they did on Palaven," she forced out. "So you think we should twiddle our thumbs while people are out there dying?" she demanded, staring them down in turn, nearly pleading.

Miranda shook her head. "We won't be idle, Commander. The Normandy needs repairs. We need to resupply. The Citadel must have its own problems too, with the number of refugees and wounded that are undoubtedly arriving."

Shepard glanced at the others, considering. "What do you two think?" Her voice was already calm again, though all present knew how deceptive that could be.

Liara cleared her throat. "I have contacts you could meet with," she offered. "There are always tasks that need doing. A Spectre has access to so many resources."

Shepard regarded her carefully before nodding. "Garrus?"

He shrugged. "I'd welcome the chance to help out the refugees. Whatever crew isn't busy with repairs can make themselves useful."

"Fine," she relented, though her voice was tight. "Miranda, talk to Tali and create a roster for repairs. Make sure everyone has a few hours of shore leave booked in. Garrus, contact the people in charge of the refugee camps. I need to be certain our crew will be a help and not a hindrance. And Liara, I want you to get me a list of people I should meet with. Understood?"

The two women answered with a "Yes, Commander," and Garrus with a salute. She dismissed them, sagging back against the metal wall. She took a few moments to reframe her expectations. Two days of work on the Citadel and then her meeting with the council. And if the meeting didn't go as she wanted it to, well, breaking out was still an option.

But she wouldn't dwell on that. She hadn't slept since before Menae, and if the meeting she'd just finished was anything to go by, it was beginning to affect her decision-making. It was time for a nap while she waited for her officers' reports. She yawned as she made for the elevator. Delegation was a hell of a thing.

…

Shepard woke up to the sound of a ping on her omni-tool. She rubbed her eyes and then pulled up the display, unsurprised to find Liara's list of Citadel contacts. Some were those she could help, and some might be of help to her. She quickly dressed and headed towards the airlock, intent on making contact with at least a couple of them before the day was done.

When Shepard reached the airlock doors, she was surprised to see Garrus waiting there for her. "I was hoping to catch you before you left," he said as the doors opened. He motioned for her to step inside, following her as she did.

"Primarch Victus is going to speak to the council on your behalf," he said as the decontamination sequence commenced.

Shepard turned to stare at him, hardly believing her own ears. "On my behalf? I can't imagine why he would." Her eyes locked on his in realization. "What did you say to him?"

"I told him the truth," he said simply.

She closed the distance between them. "And what is that?"

His voice was soft and firm. "He asked me if I trusted you with my life. I said I trusted you with the galaxy."

Her chest felt tight and her throat thick. She blinked hard to hold back tears. "Garrus…"

He tucked an errant lock of hair behind her ear, humming gently. She fell silent, words failing her. She was nearly crushed under the weight of that trust. He, who knew her best, still had more faith in her than she could fathom. Didn't he understand how she faltered? Hadn't he seen her fail and struggle?

"Thank you," she said finally, finding her voice as the door opened. A brush of talons across her cheek and he was gone. She took in a shaky breath and straightened her shoulders before following him from the airlock.

…

About halfway through the second day of Shepard's enforced stay at the Citadel, she got a message from Miranda on her omni-tool. Shepard frowned at the display as she read the message—only a set of coordinates and a time. She knew Miranda wouldn't ask something of her that wasn't necessary, but she wished Miranda had given her at least a little information about what to expect.

She frowned even harder when she saw that the coordinates were for an asari nail salon. "Good, you made it," Miranda said briskly as she approached her.

"What's this all about?" Shepard asked as the brunette hustled her inside.

"We have an appointment in about two minutes. Everyone scheduled shore leave hours but you, Shepard," Miranda said in an undertone before turning to the woman at the counter with a smile. "Hi, we have appointments for three under the name Lawson."

"Three?" Shepard asked, her arm still in Miranda's tight grip.

"Kasumi is joining us."

"Right this way," said the receptionist. She led them to a set of pedicure chairs and got Shepard and Miranda set up. A few moments after she walked away, Miranda shot Shepard a look. "You're working," she said.

Shepard rolled her eyes. "No I'm not. You won't let me. I'm getting my nails painted." She wiggled her toes to prove her point.

"You're thinking," Miranda countered. "For you, that's the same as working. Stop it. This is shore leave."

"Miranda," she said deliberately, "do you see a drink in my hand?"

Miranda looked at her cautiously, not sure where the commander was going with this. "No?"

Shepard smiled triumphantly. "Then it's not shore leave."

A few moments later, Kasumi materialized next to them with several fruity drinks in hand. She passed one to Shepard. "Better?"

Shepard looked from Kasumi to Miranda suspiciously. "What is this, Operation Keep Shepard Sane?"

When a look passed between the two women, Shepard winced. "It is, isn't it?" She sighed. "Tell me I'm not that bad."

Miranda and Kasumi shared a significant look, and all three women burst out laughing.

"Thank you," Shepard said, when the laughter had subsided. "For keeping your crazy commander in line." She was quiet for a moment as she sipped her drink. "So… any idea how long this is going to take? I've still got some people to meet with, you know."

Miranda and Kasumi groaned.

…

The following day, Shepard met with the council a second time. Despite their many misgivings, they released the Normandy from lockdown. She'd received a scathing lecture from them, but they didn't seem inclined to punish her in any way for her actions, at least not with the war ongoing.

Shepard made a mental note to write Primarch Victus one hell of a thank you message.

When she boarded the Normandy, EDI let her know that Hackett was waiting for her on the QEC.

"Admiral," she acknowledged, saluting him out of habit. "What can I do for you?"

"Shepard, I'm aware that you are currently brokering alliances between races, gathering leaders for a summit of some kind," he said. "I'd like to send a representative of the Alliance to work aboard the Normandy. Someone who can keep abreast of what's going on and keep in contact with me so that you don't have to."

Shepard's brows rose, surprised at such a request, but gave it a few moments of thought. She was wary of Admiral Hackett at the moment—he seemed to feel that she owed him her help simply because she was human. She did know that he'd watched out for her and advocated for her during her military career, but then again, he'd never been shy in asking her for favors.

After a moment of thought, she determined that this request didn't seem unreasonable. "So long as the rep pulls their own weight here, I don't see any problem with it," she told him. "They can have a trial run, but I want you to understand that I'm going to extend the same courtesy to each of the other council species as well."

A hint of a smile curved his lips. "I wouldn't expect any less from you, Shepard. I'll send you the dossier."

"So long as they can board before our departure at 0900 tomorrow morning, sir."

"I'll make sure he knows."

Shepard headed up to her quarters, and her omni-tool pinged just as she stepped inside the room. She pulled up the dossier and swore.

Kaidan motherfucking Alenko.

…

Garrus hurried up to Shepard's quarters, wondering what could have set her off. The entire crew was aware that the lockdown had been removed. They had a scheduled departure for the following morning. So what triggered the urgent message she'd sent him?

Garrus entered the room, moving down the stairs into the living space where Shepard paced back and forth. When he reached the bottom of the stairs, she chucked a datapad at him that he barely caught before it hit him.

He hesitated before looking down at it, more concerned with her state of mind than whatever could be on it.

"Read it," she said, her voice clipped.

Never one to disobey her orders, he began to do so, and quickly understood what had caused her agitation.

Unfortunately, he had no idea what to say. They had never discussed Kaidan.

Garrus remembered the way the two of them had been back on the original Normandy. They had tried to keep their attraction quiet, but it could be seen by those who were looking. Though Garrus hadn't identified his own interest in Shepard until after her death, he had always watched her closely. Back then she was his hero, his idol.

He was there that day on Horizon as well, and saw their confrontation firsthand. When it was over, he rode back to the Normandy with her, stony-faced and silent. He found her slumped over the ship's bar, drunk and angry, and made sure she got back to her quarters, worrying all the while that he'd overstepped his place.

When Garrus came out of his reverie, he found her still pacing. He set down the datapad, trying to figure out what to say.

Shepard looked at him and shook her head. "Hackett probably thought he was doing me a favor. He couldn't be more wrong. I don't know how I'm supposed to coexist with him, Garrus." She plopped down onto the couch, dropping her face into her hands. "I can't think of many people I'd want on my ship less than Kaidan Alenko."

Garrus crossed his arms and raised a browplate at his mate. "The Illusive Man?"

Shepard looked up at him, gaping. "What the fuck, Garrus."

"Khalisah Bint Sinan Al-Jilani?" A smirk began growing on his face.

"Ew, that bitch?"

"Udina?"

"Shit, don't give me nightmares, Vakarian."

"Harbinger?"

She burst out laughing. "Alright, big guy, I think you've made your point."

When she turned her smile on him, he couldn't help returning it in kind. The galaxy was falling to pieces, but he could still make her laugh.

"In all seriousness, Shepard, it's hardly going to be fun for him either," he reminded her. "No one on this ship will be happy to see him." He sat down beside her.

She grimaced. "Does everyone know about Horizon?"

"That he was an ass down there?" he asked. "Pretty much, yeah. If you're asking if they know that you and he…" He trailed off, trying to hide a grimace of his own. "Not sure. Can't imagine the crew would want to discuss that with me." He looked down at his hands.

She shifted closer to him and reached out to lift his gaze to hers. Her eyes were soft and serious as she caressed the scarred side of his face. "What I had with him… it was nothing compared to this," she said quietly. "There's no one but you. You know that, don't you?"

He closed his eyes and leaned into her warm, gentle hand. "I know, Jane," he said. And yet, it meant everything to hear her say it. "We'll deal with this the way we deal with everything else."

She smiled at him, that luminous smile that was so rare. "Together."

…

Miranda stood just inside the airlock, waiting for the doors to open. She didn't fidget—she never did, it was unbecoming—but she did release a small sigh of impatience.

She straightened slightly as the doors opened, revealing a somewhat uncomfortable Kaidan Alenko in a pristine Alliance dress uniform, two footlockers at his feet.

Miranda stepped forward. "Welcome to the Normandy, Major Alenko. I'm Miranda Lawson, the Normandy's executive officer." She reached out a hand to shake.

Kaidan's hand remained by his side as he glared. "I know who you are. You're Cerberus," he spat.

"Ex-Cerberus," Miranda corrected calmly, lowering her hand. "If you'll follow me, Major Alenko," she said, motioning him ahead.

"I'm not going anywhere with you, Cerberus," Kaidan protested, perturbed. "Where's Shepard?"

Miranda stepped forward, looking Kaidan in the eye. "Let me make this clear. When the captain orders me to show our Alliance representative to his quarters, I intend to do so," she stated. "Everyone on this ship follows orders, Major, and when Shepard is unavailable that falls to Deputy Commander Vakarian and myself," she told him, rather enjoying the way his eyes widened at Garrus's name. "If you wish to meet with Shepard, it will have to wait until after her current meeting is finished. Now would you like me to show you to your quarters or would you rather wait here?"

With a final glare in Miranda's direction, Kaidan turned and walked towards the elevator. Behind his back, Miranda rolled her eyes. At least he didn't ask about Shepard's 'meeting'. He really didn't need to know that Shepard's 'meeting' was, in reality, a leisurely breakfast with Garrus in her private quarters. Miranda understood perfectly how Shepard and Garrus might feel the need to reaffirm their relationship at such a time. And while Miranda didn't necessarily consider herself an advocate for interspecies relationships, she was definitely an advocate for anything that made Shepard's job—and therefore her own—easier. And tweaking Alenko's nose? That was just a bonus.

About an hour after leaving port, Shepard came into Miranda's office. "Hey," she said. "I understand you got Alenko all settled in."

"I did," Miranda replied, though she was a bit surprised that Shepard still hadn't gone to see for herself. "I admit that I do feel some concern about him. I'm not certain he will adjust to our ex-Cerberus crew."

Shepard sat down across from her. "If he doesn't adjust, he doesn't stay. I'll mention it when I talk to him," she assured her.

"I appreciate it, Commander." Miranda went back to typing up the report she was working on, and wondered if Shepard had any other purpose in coming to see her. Silence reigned for several minutes until Shepard spoke up suddenly.

"Have I lost my way?" she asked.

Miranda leaned back in her seat, surprised at the question. Was it Alenko's arrival that made her doubt herself?

She watched Shepard with a speculative eye. "Why ask me that, Commander?" She carefully added, "I would expect you to be more interested in the opinions of someone like Tali or Garrus."

I didn't think you held my morals in such high regard, was left unsaid.

Shepard gave her a small, sad smile. "You have no illusions about me, Miranda. No hero worship or ingrained loyalty. You're logical to a fault. The only thing that clouds your judgment is Oriana."

Miranda bit back her surprise at such a stark portrayal of her character, somewhat saddened by the implication that her time with Shepard had earned her no loyalty. She wondered if Shepard was giving her too much credit or too little with such an assessment. She set her personal concerns aside and considered the question.

"This war is going to be messy," she said after a moment. "Not everything will be simple. Rules will be broken, some that may seem morally distasteful. We can't allow that to be the stumbling block that kills us."

Shepard looked for doubt in Miranda's eyes. "And if we lose our humanity along the way?" she asked. "Is it worth it then?"

She met Shepard's gaze without hesitation. "There isn't room for that kind of questioning here. We'll do what we have to in order to survive. Anything less is failure."

Miranda followed Shepard's gaze as it dropped to her hands. The commander stared at them, as if she could see the blood she'd spilled over the years coating her fingertips. The galaxy didn't just need a hero. They needed someone who could get their hands dirty when the time came. Shepard was still trying to be both, but Miranda feared a day would come when she would have to choose.

She only hoped it wouldn't break her.

…

A/N: I have been posting some incomplete stories on my old Tumblr lately (same user name) with the tag "stories that will never be finished"—since I don't post anything on this site or AO3 that I don't feel confident I can complete. If you want to read more of my work (and don't care if the stories are unfinished), I recommend taking a look.