Running Silent:

Separate Ways

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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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Shepard knew Garrus far too well to be unaware of his nervous fidgeting and conspicuous attempts to hide a grin.

She puzzled over it. He couldn't have anything else planned for their shore leave—they were on the way back to the Normandy. She guessed it was something back on the ship, but for the life of her, she couldn't figure out what. They arrived at the docking bay, both anticipating what was to come, though only one of them had any idea what exactly that was.

As they rounded the corner, the Normandy came into view, and Shepard sucked in a sudden breath. Sharp angles and Cerberus yellow were gone, replaced with a swooping blue like ocean waves or the soaring arc of a biotic field. The ship's white panels shone like new, reminding her of that day when she'd seen the first Normandy gleaming in an Arcturus docking bay.

Shepard had always loved ships. As a little girl, she would run off to the spaceport every time a new ship docked, just to get the chance to see it. After all these years she still could never quite escape the allure of a gleaming ship, ready to soar off into the unknown.

She felt him come up beside her. "It's the same color as your eyes," he said softly in her ear.

Those eyes snapped to him with a curious expression. Shepard had approved a repaint to remove the Cerberus logos and cover the repairs, but she'd never imagined they would redesign the Normandy so beautifully.

"You matched a ship to my eyes," she said wonderingly. "I think that's the most romantic thing anyone's ever done for me, Garrus." She laughed gently, but she was genuinely touched. She wasn't one for romantic gestures, for flowers and chocolate and candlelight dinners. She didn't care about those kind of things. But a ship—that was something she loved.

"Come on," Garrus finally said, tugging gently at her elbow. "There's more."

Shepard's brow creased as she followed him to the docking tube. "What do you mean 'more'?" she asked, but the only answer she received was a grin.

Tali and Miranda met her at the airlock, the quarian nearly vibrating with excitement.

"Sorry we're late," Garrus said by way of greeting. "I had to drag her away from the viewing platform," he explained.

The woman in question crossed her arms, shifting her weight back onto one leg. "So when Garrus said there was more to see, I'm guessing he didn't just mean the finished repairs."

She swore Tali was grinning inside her helmet. "Come and see," she said.

The Normandy's executive officer led the way as she headed the elevator and silently pressed the button for the first deck—the captain's cabin.

Shepard lowered a brow. "I swear to god, if you guys moved any of my stuff—"

EDI's simulated voice filled the elevator. "I can assure you, Commander, that all of your possessions have been returned to their original positions, aside from your copy of Fornax."

Shepard blinked incredulously, feeling the turian beside her suddenly go stiff. "My…what?"

Tali dissolved into a fit of giggles, and even Miranda was smirking. EDI's voice was smug when she spoke up again. "That was a joke."

Shepard glared at Miranda and Tali as the elevator door opened, the quarian still laughing uncontrollably. "Oh, Keelah," she gasped out between giggles. "Your faces!"

Shepard didn't dare look at Garrus, but she crossed her arms and waited for Tali's fit of laughter to finally die down. "You had something else to show me?" she asked coolly, raising a brow at the quarian who had barely gotten her laughter under control.

Miranda, composed as ever, led the way into her quarters, motioning immediately to the right. When Shepard came around the corner, her lips spread into a grin, her annoyance forgotten. The wall beside her desk was gone, replaced by a glass case with enough room to double her model ship collection.

She turned to face her friends with a smile. "Forget what I said yesterday about hating you two," she said, throwing her arms wide. "I love you guys!"

…

The light was dim in Shepard's cabin as she filtered through her most recent batch of messages. Councilor Anderson wanted to meet with her alone, an Alliance rep wanted her to forward something to Jack of all people, and Admiral Hackett wanted her to call him when she had some time available.

She yawned and stretched, far more interested in bed than her messages. Her day back on the ship had been a busy one. They'd lost a couple more crewmen during this stop. In total, thirteen people had decided to leave the Normandy, which was pretty good, all things considered. The crew had been through a lot, more than they'd signed up for. She was impressed with anyone who wanted to stay after the ordeals they had endured. She'd promised them no questions asked, but every member of the departing crew had gone out of their way to tell her why they were leaving. Kelly Chambers had been the last.

"Who's going to feed my fish now?" Shepard had asked, trying to bring some levity into the situation despite the surprisingly heavy feeling in her heart.

Kelly just smiled, understanding so much more than she let on. "I have faith in you, Commander."

She'd wanted to protest, but all she did was squeeze Kelly's hand in goodbye.

Her door chimed, and Shepard leaned back in her chair. "It's open," she called, but the door remained closed. She sighed, spinning her chair to face the doorway. "You can come in," she added loudly, trying keep the annoyance out of her voice.

When nothing happened, she rolled her eyes and stood, going to open the door herself. When the panels separated, she saw no one. Was EDI branching out into pranks now?

As she was about to turn away, she saw the box on the floor in front of her. She picked it up curiously, read the label, and smiled.

Because faith doesn't feed fish. –K

Still smiling, she brought the box into her quarters and set it on the desk. Shepard peeked inside, laughed out loud, and pulled up her omni-tool.

"Tali?" she called, having no doubt the quarian was still up and working.

"Yes, Shepard?" came the response. She could hear tools clanking in the background. Dear, predictable Tali.

"Need you for something," she told her.

"It's not another invasion of Kasumi's bar, is it?" Tali asked skeptically, remembering the last time Shepard called her for an 'important mission' this late in the night cycle.

Shepard laughed at the memory. "Not this time," she reassured her. She looked at the box and smiled. "I've got a VI that needs installing."

…

Every single member of her crew protested when she brought up her plan.

She had the same argument over and over. No, you can't stay. Yes, you can do it. I believe in you. I'll be fine, I promise. I'm coming back for you.

In the end they'd all come around, some more reluctantly than others. She made the assignments—Garrus to Palaven, Tali to the Migrant Fleet, Mordin to STG. Legion wanted to bring his experiences back to his people. Jacob thought he might have some leads with a few ex-Cerberus friends, and Jack had accepted a surprising offer to teach biotic students at Grissom Academy.

Miranda was staying onboard. The 'I cant leave, you need someone watching your back' arguments fell apart when Shepard assured her team that the XO would be remaining with her. Though each member of her crew was insistent that they ought to be the one watching their commander's back, Shepard knew she had made the right choice. Unlike most of the team, Miranda's defection from Cerberus was personal. Shepard didn't like the idea of sending Miranda out on her own when the Illusive Man was hunting her. Besides, no one else would have been so much help running the ship and hiring new crew.

Only after she'd made this decision did Shepard find out that Kasumi had no intention of leaving either. "No one else takes me to such nice places with so many shiny things," she'd teased. Shepard had a suspicion that there might be more to it—Kasumi had led a lonely life, and the Normandy had been like a family for all of them. Despite her occupation, Shepard quite liked the thief and would be glad to keep her around. With both Kasumi and Miranda staying, Shepard had a full combat squad—which silenced the last of her team's protests.

Shepard hadn't quite figured out why Zaeed Massani was still hanging around her cargo hold after the mission was finished and he'd been paid. She wasn't sure how exactly she'd earned his loyalty, but whatever the reason, he had stuck around. Though he did tell her he was leaving—"for some well-earned goddamn vacation"—he'd made it abundantly clear that he'd be returning soon. "Don't fuck up my room," he'd said by way of goodbye.

After she dropped her team off where they wanted to go, Shepard intended to make the trek out to Tuchanka in hopes that she could convince Wrex to let her keep Grunt with her on the Normandy. At their parting he'd told her to "bring that boy back alive", but she had no intention of sending Grunt away if she could avoid it.

Once that was settled, she had a few small errands to run and missions to complete. There were a few more minor repairs and tweaks to be made, and she needed to fill in the gaps left in her crew. Foremost in her mind, however, was the favor that Admiral Hackett had asked of her. With the promise of Hackett's gratitude and evidence for the reapers, it could be exactly what she needed.

Everything was falling into place for her plan—but even though this was what she had wanted, Shepard wasn't happy.

Because the plan meant saying goodbye.

…

"Writing to your boyfriend?"

Tali'Zorah vas Normandy looked up from her omni-tool to see a turian smirking at her from the doorway. She quickly shut down the orange interface and glared at him. "Like you can talk, lover boy. And Kal'Reegar is just a friend."

Garrus grinned as he approached with his usual cocky swagger. "But you did know who I was talking about."

She shoved him playfully, smirking behind her helmet as he stumbled. "Bosh'tet."

He let out a laugh as he regained his composure, but seriousness soon filled his eyes. "You going to be okay going back there after the trial?"

Tali huffed in annoyance. "I'll be fine," she insisted, planting her hands defiantly on her hips. "Keelah, first Shepard and now you. You don't need to fuss over me, you know."

"I didn't know Shepard said anything," Garrus said defensively. "And I can't help looking out for you sometimes. I've got a younger sister. It's an old habit."

Tali's bright eyes widened behind her helmet, completely distracted by his offhanded comment. "You never told me you had a sister! What's she like?"

Garrus grimaced, already backing away. "You win. I won't fuss." He moved to leave the room quickly, but paused to call back over his shoulder. "Just tell that boyfriend of yours that he better be good to you because if he doesn't, Archangel will come after him."

Tali huffed again as the doors shut behind him. "Bosh'tet."

…

A steady stream of people broke around Shepard and Garrus as they both tried in vain not to think too much of the last time they'd stood in a docking bay to say their goodbyes.

Their first parting hadn't carried the weight this one did, nor the emotion. They had just survived the impossible, still riding high from their victory against Saren. The idea that they wouldn't see each other again had been a laughable one. They knew better this time.

"You'll be back on the Normandy before you know it," she promised, though disquiet hid behind her placid countenance. Did he know she was afraid? If he did, would he demand to stay?

He reached out for her hand, clasping it between both his own. "Don't do anything stupid without me to watch your six," he warned. "If you get yourself killed because I'm not there…" His thumb stroked across the back of her fingers.

She squeezed his hand. "I'll be fine, Garrus. I promise."

He shook his head. "I'd ask you to be careful, but we both know that would be an exercise in futility. Just make sure you get out of whatever messes you get yourself into, okay?"

She couldn't hold back a smile. "I'll do my best."

The loudspeakers crackled to life, calling for his transport to board. "I have to go," he told her, but made no move to leave.

Shepard impulsively stretched up and placed a kiss on his mandible. Maybe she shouldn't have—they'd agreed on no displays of affection, not somewhere so public. But in that moment, Shepard couldn't say she cared. "I'll miss you," she whispered. "But we'll be back together before you know it. Shepard and Vakarian, right?"

"Shepard and Vakarian," he said, like a vow. For just a brief moment, Garrus pressed his brow to hers. "Goodbye, Jane," he whispered in her ear, and turned to head to his transport. Shepard's eyes followed his receding form until he disappeared from sight.

She walked back slowly, not quite wanting to get back on the Normandy without him on it. She felt strangely vulnerable now, without him there to watch her six. But she reminded herself of her own words—it was only a short time before he would be back by her side where he belonged.

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A/N: Next chapter we visit Tuchanka, Palaven, and more!