Running Silent:

An End and a Beginning

…

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 burst into the forward battery to find Garrus sitting on his old cot, slumped over with his face in his hands. Before he could do more than look up at her, she was seated beside him, pulling him against her chest. "Miranda told me. I'm so sorry, baby." He was trembling, but no sound escaped him. After a moment, he returned the hug, holding Shepard tight.

"I thought," he rasped out, "I thought she was going to get better. Or that we'd have more time. The treatment—" His subvocals keened his grief when he couldn't speak.

"I know," Shepard whispered, placing a kiss upon his crest. "Where's Solana?" she asked after a moment.

"In her room," he said. "Tali's with her."

"She'll take good care of her," Shepard agreed, remembering Tali's grief at her father's passing the year before. "She knows what it feels like."

She held him for another long minute before speaking up again. "Will you come up to my cabin? Let me take care of you?" she asked. "Please."

For the first time, Garrus looked up and met her eyes. Shepard felt sick at the pain in them. When he nodded his agreement, she took him by the hand and led him up to her room.

…

Shepard stroked over Garrus's fringe as he lay sleeping beside her, hoping his dreams were more pleasant than their reality. He was devastated at the loss of his mother.

Shepard forced her thoughts away from Garrus and tried instead to focus on the datapad in her hand. She needed to catch up on the time she'd been away. The news from around the galaxy wasn't good.

The vorcha reapers they had seen on Earth, now known collectively as the horde, were being found on more and more planets, swarming over cities and destroying nearly everything in their path. They had powerful jaws and claws, and their numbers were difficult to defend against. Current recommendations were grenades and flamethrowers.

Their armies were not faring well against the reapers either. It seemed that Admiral Hackett's move to pull back from Earth was a good one. Other races were now following his lead and reducing their presence in the home systems to little more than what was needed to facilitate evacuation. Shepard believed that every government would soon take this action, especially since there was no guarantee now that their homeworlds would survive this war even if their people did.

Shepard yawned, and Garrus shifted beside her. With another glance she turned off the datapad, sliding under the covers and wrapping her arms around him. She felt helpless in the face of his grief. She would do anything in the galaxy to help him, but all she could do was hold him while he mourned.

Later, when they both woke, he seemed a little more inclined to talk. "When does it stop hurting?" he asked. "How long?"

Shepard sighed, staring out through the skylight. "It doesn't stop, really. Over time it just fades into the background until you can forget sometimes. It becomes part of you."

"How long did that take when you lost your parents?"

She gave him a sad half-smile. "I'm hoping it will be different for you. You still have people around who love and care for you. For me, it wasn't just my parents. It was my home, everyone I'd known. And… my little brother."

Garrus blinked, staring at her. "I didn't know you had a brother."

"It's not something I advertise," Shepard admitted. "I don't like to talk about him much."

He looked down again. "I won't make you," he said, but she could tell he wanted something to take his mind off his own grief.

"I was five when my parents told me I was going to be a big sister," she volunteered. "They named him John Randall Shepard. I wanted to name him Michelle." Shepard smiled a little at the spark of laughter in Garrus's eyes. She shrugged. "I really wanted a sister."

"He loved ships, even when he was just a baby. His favorite thing was going to the spaceport and watching the ships take off. He always wanted to play like he was a pilot," she continued.

"I take it you got over him being a boy?" Garrus roused himself to ask.

She smiled. "Eventually. I preferred playing pilots with him to playing dolls with my friends' younger sisters, anyway."

"Why don't you like to talk about him?" Garrus ventured. "It seems like remembering him makes you happy."

Her smile dropped. "My parents managed to save me from the slavers. But the last thing they asked me was to find my brother." She shook her head, blinking hard. "I didn't save him."

"I'm sorry," he said. "I didn't mean to make you relive that."

"I'm alright," Shepard insisted. "It was a long time ago. I'm more worried about you."

Garrus gave her a bleak smile. "I'll be fine. Like you said… I just need time."

…

Shepard stepped into Mordin's lab, feeling emotionally exhausted from the past few days. "How's your progress, Mordin?" She looked around, glad to see the lab up and running again.

"Studying samples with data from Maelon's experiments," the salarian said. "Can reverse genophage modifications easily. Created those myself. Working on improving natural resistance. Much harder. Excellent challenge!" He smiled brightly, his hands still typing away.

"Glad you're enjoying yourself," Shepard said, humor in her voice. "Do you need anything from me?"

Mordin hummed in consideration. "More data, if possible. Maelon's experiment can't be only one. Also data from original genophage may still exist. Research. Discovery!"

She smiled. "Alright, Mordin. I'll have us looking for anything else there is to find. I'll get you all the data out there." She shifted stance. "But… I was wondering something. What changed your mind? Only months ago you insisted that updating the genophage was the right thing to do. And now we're working to undo that. Why?"

Mordin sniffed, and was silent a moment. "You. Grunt. Urdnot Wrex." At Shepard's frown, he continued. "Always told krogan couldn't be trusted. Had to be controlled. Couldn't handle gifts we gave when we uplifted them. You argued, told me I was wrong. Demanded I see other side of things. Fresh eyes."

"And Grunt and Wrex?" she ventured.

"You asked me to look. Saw krogan who weren't mindless fighters. Had vision for future. Cared about others. Learned krogan aren't hopeless." He paused in his work and smiled at her. "Can still learn, even at my age."

Shepard couldn't help smiling back. "I'm glad to hear that. There's no one I'd rather trust this with."

"Thank you, Shepard." He turned back to his work. "Good to be back."

"Good to have you back," she replied. She felt a weight lift from her as she left the lab. It felt good to be working on something not morally ambiguous for once.

…

Liara flickered into view on the QEC. "Shepard," she said. "I've been looking into what you asked. I've got data from a number of experiments for you. And, well…" She wrung her hands anxiously. "After a bit of a hunch, I tracked down Maelon Heplorn, the young salarian who performed those experiments you stopped on Tuchanka."

Shepard frowned slightly. "He better be running a nice, quiet clinic on Omega, like Mordin told him to."

While that is true, I am afraid that is not all he is doing."

Shepard sighed, rubbing her forehead. "You're kidding."

"I'm afraid not. He is once again looking into a cure for the genophage—backed and protected by the Blood Pack."

Shepard huffed a laugh. "Well. He's got more guts than I gave him credit for. We should probably stop whatever he's doing and gather his data while we're at it. I'll talk to Mordin." She moved as if to leave, then stopped. "Liara? How are you holding up?"

The asari gave her a small smile. "I am as well as I can be, Shepard."

"I know you don't want to have to rely on Project Pyrrhus," she said, concerned, "but you need to sleep sometime. Trust in our scientists, Liara. They'll get it done."

Liara shook her head sadly. "How can I trust in them when I can see that you do not?"

Before Shepard could say anything more, the feed went dark.

…

Garrus and Solana sat together as they spoke to their father on the comm.

"I'll be taking your mother back to Palaven for a proper funeral rite," Castis said calmly, to immediate protests from both his children.

"It's too dangerous to go back right now!" Solana cried.

"And there's no guarantee you'll be able to leave the planet again safely," Garrus added.

Castis held up his hands, shaking his head. "This is not up for discussion. I am taking your mother back to Palaven for a proper funeral. You are not to attend. You will stay where you are. And when I'm finished…" He sighed. "I will stay where I am."

Garrus stiffened. Solana glanced at him, worried, but continued voicing her concerns to her father. "It's so dangerous there, Dad. And shouldn't you stay near the primarch? You've always advised him."

"That was the old primarch," he said, and glanced at Garrus. "The new primarch prefers the counsel of your brother. And it is not for me to say that he is wrong." He sighed. "Palaven has been my home for most of my life. I'm determined to stay and defend it."

After a moment of silence, Garrus leaned forward. "Dad," he said urgently. "Promise me something. If I call and tell you to get off world, do it. Don't wait." His intensity was unmistakeable.

The elder Vakarian's eyes were unreadable as he gazed at his son. "I will. Now, do good work and take care of each other."

"We will," Solana promised, and Garrus added his nod. Castis smiled slightly before the feed went dark.

Garrus began to stand, but Solana pulled him back down. "Why don't you want Dad on Palaven, Garrus? What do you know?" she demanded.

…

When Shepard was working in her quarters alone, EDI's interface popped up at the side of the room. "Commander, may I ask you something?"

Shepard pushed back from the computer. "Go ahead."

"When you spoke to Liara earlier, why did you lie?"

She tilted her head. "About trusting in the scientists?"

"Yes. You do not believe that the weapon will work, but you tried to make Liara believe it will. Why?"

Shepard was quiet for a moment, considering her words. "Liara is struggling with the plan. She's overworking herself, not sleeping, probably not eating well either. I want her to take care of herself because the war needs her at her best." She paused, smiling sadly. "And because she's my friend."

"But isn't honesty between friends important?" EDI persisted.

"It is, but…" Shepard struggled to explain. "Sometimes you have to weigh that against other factors. If Liara had no hope of saving Thessia, she might not be able to go on. So I try to give her that hope, no matter how much I doubt. I'm trying to help her, to take care of her the best I can. Sometimes that means not being fully honest." She paused, worried about how far EDI might take her advice. "But I never keep something from her that she needs to know. I could have kept Project Pyrrhus from her completely, but that would have hurt her and the war effort more than it would have helped by sparing her the worry. Do you understand?"

"I see," EDI replied. "I will consider this carefully."

"If you have other questions, you can come to me," Shepard assured the AI.

"I am sure I will," EDI said. "Organic beings are a fascinating study. Logging you out, Commander." And the blue interface blinked out.

Shepard shook her head. EDI had a long way to go before fully understanding people, but she sure was trying.

…

Shepard sat across from Miranda, discussing the upcoming mission. "I think we can recruit Maelon as well as acquire his research," she said, "but I'll have to see what the situation is on the ground."

"There's just one problem," Miranda said dryly. "We can't dock on Omega. Aria was furious that we brought Cerberus down upon her there, and she won't take kindly to us endangering Omega again."

"It'll have to be stealth, then," Shepard considered. "Have O'Connor take us on the shuttle. Kasumi can dig up some fake identification for Mordin and I. It'll be a piece of cake."

Miranda shook her head. "If you insist, Shepard."

"What, you don't think I can do it?"

A smirk played at the edge of Miranda's mouth. "I think you're about as subtle as an elcor. Maybe someone else should go in your stead."

"I can do subtle," Shepard insisted, ignoring Miranda's raised brow. "And it has to be me. I saved Maelon's life. I believe he'll trust me."

"Very well," Miranda conceded. "But do be careful. Cerberus has always had a presence there, and it won't do you any good to be discovered without the backup that the Normandy can provide."

"Trust me," Shepard said, "Everything's going to be just fine."

…

"Aria's going to know," Garrus said, helping Shepard put on her black and red Terminus armor. "You won't be able to hide your identity from her."

Shepard snapped on her gauntlets before replying. "Aria won't care as long as no one else knows. She just wants to make sure that Cerberus doesn't all flock to Omega."

"She'd probably be pretty pissed off about Harbinger, too," Garrus reminded her, helping Shepard fit her back plate.

"No one's going to find us," she assured him. "I'll be subtle."

Garrus snorted. "Of course you will." Then he sighed quietly, stepping back. "I wish I was going with you. I just keep getting this feeling that something will go wrong if I'm not there with you."

"Everything will be fine," Shepard insisted, turning to grasp Garrus's arms. "I promise. And I'll call every night we're gone."

"If you don't, I'm bringing in the cavalry. So you'd better call."

Shepard picked up a bag and headed into the elevator, Garrus on her heels. "Any last minute advice?" she asked.

"Oh, plenty," Garrus said wryly as the doors closed. "But I'll just say one thing instead. Listen to Mordin. He knows Omega and won't steer you wrong."

She smiled. "I will," she said, and stepped forward to kiss him. "I hope this won't take long," she added quietly as the doors opened to reveal the Normandy's shuttle bay. "I'll miss you while I'm away. Take care of yourself, Garrus."

Miranda, O'Connor, and Mordin met them when they exited the elevator. "Garrus is in charge of missions while I'm gone," Shepard reminded Miranda. "I believe you were going to pick up a few things that the council thought might be useful in our fight?"

"And talk to STG about getting some of the original genophage data. Once we're finished, we'll rendezvous in the Hourglass Nebula like we discussed," Garrus said.

"You're in charge of ship operations, Miranda," Shepard added with a nod. "The two of you need to work together. Call me if anything unusual happens."

"That goes likewise for you," Miranda insisted. "You'll let us know if anything goes wrong. We won't be far, so the Normandy can come in if need be. Keep a constant eye out for Cerberus and be careful never to use your real names. They have people all over Omega."

"Will do," Shepard agreed. "See you in a few days."

At that, Mordin and O'Connor boarded the shuttle with Shepard a moment behind. "I'll be careful," she added to a waiting Garrus. "I promise." And she shut the door.

…

Shepard and Mordin tried to look casual as they left the dock. "We're being watched," she said quietly.

"All new arrivals watched," Mordin replied. "Aria's people. Visit Afterlife first, maybe lose interest."

She tapped her helmet. "Can't exactly stop by for a casual drink, remember?"

"Shopping, then!" he said, quickly turning towards the district.

Shepard shook her head, but followed his lead. Mordin was easily distracted, examining a variety of black market products. Shepard wasn't so easily drawn off course. "We should get a move on. They won't follow us into blood pack territory," she was sure.

"May look suspicious though," Mordin added.

"We should still do it before Aria requests my company for a lecture or a favor. Or before she kicks me off the station again," Shepard said quietly, antsy to get on with their task. She didn't like being away from her crew for long, and who knows how long it would take to convince Maelon to come with them or at least let them copy his data?

After a stop at one last shop that Mordin insisted he needed to visit, they wound through the rabbit's warren of hallways until Shepard would have been long lost without their map. Mordin didn't seem to have any trouble navigating. "Blood pack territory soon, be cautious," he warned.

"They've expanded, haven't they? I thought this all used to be Blue Suns."

Mordin nodded. "Archangel's doing. Eclipse, Blue Suns lost millions in credits. Blood pack breeds more vorcha."

Shepard hummed thoughtfully, wondering how Garrus would feel about the unintended effects of his last stand on Omega. At the moment she had no intention of telling him. He had enough on his mind.

After walking for a few more minutes, Shepard felt something wasn't quite right. "Too quiet," she whispered to Mordin, and slowly started reaching for her gun.

Before he could reply, she heard the sounds of metal, weapons and armor in the hallway around them. Out of a few hidden doors popped a dozen vorcha and two enormous krogan, all in blood pack regalia with heavy weapons pointed directly at them.

"Damn," she sighed, and raised her hands in the air.

…