Running Silent:

System Overload

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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 stared, dumbfounded, as Aria T'Loak stormed up to her and slapped her across the face. "Sober the fuck up, Shepard," she ordered. Garrus let out a small cry of protest as he ran up beside them, but Aria only gave him a cursory glance. "I hope you two are finished making out, because I didn't save your asses for nothing."

Shepard glanced towards the Normandy's airlock, anxious to get moving again. "What do you want, Aria?" she demanded. "We don't have time for this."

"No, you really don't," Aria agreed, the measured tone of her voice contradicted by the fire blazing in her eyes. "There are more of them coming. It's you they want, but they'll take Omega while they're at it." Her eyes narrowed as she stepped in close, her face only inches away from Shepard's. "Lure them the fuck away from my station. Now." She shoved Shepard towards the Normandy and turned on her heel, heading back towards Afterlife like a woman on a mission.

After a slight stumble, Shepard made off towards the airlock at a run with Garrus right on her heels. "EDI!" Shepard called desperately from the airlock door. "Can you hear me?"

Shepard and Garrus both winced at the sudden burst of static in their ears. "I have broken through the interference," the AI said calmly.

The commander let out a small sigh of relief. "Status report."

"There are Cerberus operatives in the CIC. I have locked down the ship," EDI told her. The dented airlock door hissed open. "Neither the cockpit or the other levels have been breached."

"And the crew in the CIC?"

"Minor injuries only. Doctor Solus and Operative Taylor have evacuated them to the lab, Commander."

Shepard rolled some of the tension from her shoulders. "How did they get in, EDI?"

"Cerberus has developed a pulse that temporarily disabled my processors. I have reconfigured so that this will not happen again." There was a short pause. "Decontamination complete. Should I open the door, Commander?"

Shepard popped the heat sink from her pistol and reloaded in a quick motion. "Do it." The doors slid open and Shepard stepped inside. At the sight of the Cerberus troops tearing her CIC apart, Shepard's expression hardened into a grim mask. Nobody messed with her ship and lived to tell about it.

There were troops working on the doors to the lab and armory with crowbars and omni-tools, anything to get to the crew. Another set worked on the elevator, trying to get down to EDI's hardware, no doubt. Shepard ripped them away in biotic fury while Garrus took the kill shots one by one. The deck shook as she slammed two soldiers to the ground, scattering a stack of datapads across the CIC floor. A shot flew wide, cracking the glass of her private terminal. The prized leather seats at the consoles were strewn with rips and bullet holes. Within a few short minutes, nothing was left of the Cerberus troops but mangled bodies and the destruction they'd wrought.

Shepard's eyes darted about the room to take a quick account of the situation. The CIC was a mess. Bodies, blood, and heat sinks were scattered across the deck, dents had been made in the doors and walls, and many of the consoles were cracked or shattered. Glass crunched under Shepard's boots as she headed to the bridge. She glanced at Garrus with a silent request, and he gave her a nod. When she turned away, she heard the metallic skid of an armored corpse being dragged across the deck.

Joker twisted in his chair as EDI's barrier dissipated, his eyes showing unmitigated relief. "Man, am I glad to see you." He looked her up and down, admiring the way her bar attire clung to her sculpted body. "Nice outfit, by the way."

"I will break you, Joker," she warned, but her heart wasn't in it. Her eyes scanned the flight console. "How well will this thing fly right now?"

Joker straightened, his hands darting to the controls. "Basic systems are up and running, Commander."

"Weapon systems? Stealth drive?" she pressed.

"Functioning below optimal capacity," EDI chimed in.

Shepard nodded tersely, her eyes glancing out the windows and then back at Joker. "There are several more Cerberus ships coming. We need to bait them away from Omega and then disappear. Can you do it?"

Joker snorted. "Please. Remember who you're talking to."

Shepard stared him down. "The ship, Joker. Can she take it?" Her fingers dug into the pilot's head rest.

Joker met her eyes with a seriousness that only showed itself under fire. "I can do it."

Shepard stayed silent behind him as he turned back to the flight console. She didn't move until Omega was out of sight and so was Cerberus.

Round one goes to Shepard, she thought to herself, but it wasn't a very comforting thought. Round two was undoubtedly coming, and she couldn't afford to let it go to the Illusive Man.

They were drifting in an uninhabited system now, waiting on orders for their next stop. "EDI," Shepard barked. "Damage report?"

EDI listed off the Normandy's issues, exacerbated by the run-in with Cerberus, and Shepard rubbed her temples in exhaustion. "Send the report to engineering," she instructed. They needed to dock again, and soon.

They could go to the Citadel, but Shepard wasn't ready for that confrontation yet. Questioning awaited them when they docked, and Shepard needed time to prepare for that meeting. They wouldn't go back to Omega—she was unwilling to risk Cerberus or the wrath of Aria T'Loak—but she needed somewhere safe, where questions wouldn't be asked and their identity wouldn't be compromised. She would have to take a chance and hope this didn't come back to bite her in the ass.

"Hourglass Nebula, Sowilo system," Shepard said tiredly. "You know where to go, EDI."

"Yes, Commander," the AI replied.

Shepard sighed, thinking of her next task. "I need locations on each member of my team," she requested. She needed to check in with everyone before heading back up to her quarters, as much as she would rather faceplant into her pillow for the next few hours. She had a pounding headache already. She mentally took down the information EDI gave her, and sighed again as she stepped out into the CIC. She'd get a glass of water when she hit the crew deck. Maybe some coffee. Even Rupert's coffee sounded amazing right now.

Shepard closed her eyes and rested her forehead against the cool wall of the elevator as she waited for it to descend to the lower levels. She mentally calculated the time until the Normandy reached its destination, figuring she could get a few hours of sleep in there somewhere. She just had to finish her rounds first. She groaned when the elevator reached the engineering deck, the pounding in her head superseding her desire to move. Against her will, she pushed off the cool metal wall, and that was the last thing she remembered.

…

Shepard woke to a mouth that felt like sandpaper, a horrible ache in her head, and the murmur of hushed voices. She didn't bother opening her eyes before speaking over them. "Where the fuck am I and why does everything hurt?" she rasped.

"You're awake," said a flanged voice, tinged with relief. "Spirits, Shepard, you scared Donnelly half to death when he found you in the elevator."

She opened her eyes and slammed them closed immediately with a groan. Must be the med bay—nowhere else on the ship was that torturously bright. She tried again slowly, squinting her eyes. Her headache intensified. Ugh.

Shepard blinked as her eyes adjusted, taking a look at her surroundings. She was on one of the med bay cots with Garrus seated beside her. She had an IV of something stuck in one hand, but that appeared to be the only thing out of place. She was fully clothed—thank god—and nothing looked or felt broken. Except her head.

"The hell did I do?" she asked hoarsely. "My head feels like the morning after shore leave."

Garrus's mandibles quirked. "That's about half the story."

Doctor Chakwas strode over with a glass of something murky. "Drink this," she ordered, and helped Shepard prop herself up. Shepard took a sip, grimacing at the taste.

Chakwas crossed her arms. "You went into battle drunk, Shepard. Somehow you managed to escape unscathed but for some serious dehydration that you neglected to take care of." She gave her patient a disapproving look. "Combined with your current state of sleep deprivation, it's no surprise that you passed out in the elevator."

She handed the now-empty glass back to Chakwas. "But there's nothing seriously wrong?"

The doctor's shoes clicked on the floor as she crossed the room. "What's seriously wrong is that you've been overworking yourself since you woke up in that Cerberus lab," she lectured. "I'm ordering some time off to allow your body to recover."

"You can't be serious," Shepard said flatly as she looked from Garrus to Chakwas, both wearing similarly determined expressions. She let out a huff. "Fine. I'll take the morning off."

Chakwas laughed dryly. "It's afternoon, Commander. You've slept nearly twelve hours already."

Her eyes widened in surprise. That was by far the longest she'd slept since coming back from the dead. Maybe she should get drunk and fight more often.

"So I'm fine," Shepard argued. "I should be able to go back to work." She went to pull out her IV, but a three-taloned hand grabbed her wrist to stop her. She shot Garrus a glare. "Traitor." She ripped her hand out of his grasp.

"What you really need is several days of rest," Chakwas said. "I've let the issue slide because we were in the middle of an urgent mission, but I'm going to have to put my foot down. This has been a long time in coming."

Shepard looked at the doctor incredulously. "No. Absolutely not. I can't waste days." Chakwas was insane if she believed Shepard would just sit around for days while the ship was being repaired and the reapers were on their way—

Chakwas took a step forward, looming over her. "I will sedate you if I have to, Commander," she said in a manner that Shepard could only call menacing.

Shepard scowled. "How long?" Anything was better than sedation. They couldn't keep watch over her at every moment.

"One week of light duty, if you keep regular mealtimes and sleeping hours," the doctor instructed. "Longer if you keep neglecting your needs."

"A week?" Shepard's blue eyes widened. "You must be out of your mind, Doc. I can't. There's too much to do. And what the hell does light duty even mean?" she asked, exasperated. "If Cerberus attacks the ship again, I'm not just going to sit in my quarters and wait it out."

"Emergencies aside, of course, it's this or sedation," Chakwas said firmly. "No missions. No late nights."

"Fuck," Shepard muttered in frustration. She looked at her two captors, feeling petulant. "If the galaxy goes to hell during my week I'm off, it's your fault."

Chakwas gave a humph that Shepard took as satisfaction. "I want you on that IV drip for a couple more hours. After that, I will release you to your quarters. Understood?" She waited for Shepard's nod—accompanied by a roll of the eyes—and looked to Garrus. "Keep her here," she ordered and turned on her heel to leave the med bay.

After a minute or two of silence, Shepard looked over at the turian beside her. "So…" she began, "How long have you been sitting there?"

Garrus's mandibles twitched slightly in embarrassment. "Pretty much since I heard what happened," he admitted. "EDI alerted me while I was cataloguing the damage to the CIC. So I rushed in here and…" He shrugged. "I've been back and forth since last night. You were completely out until a few minutes ago." Garrus smiled. "You snore sometimes. It's cute."

Shepard raised a brow. "Cute?" she repeated deliberately. The last person that called Commander Shepard cute had gotten punched. But it didn't matter anyways because he was definitely full of shit. "I don't snore, Vakarian."

He leaned back, crossing his arms. "Should I ask EDI to roll the footage?"

"Insubordination," she declared. "One day I'm going to kick you off my ship for it."

"No you won't."

Shepard shrugged, trying to hide her smile. "Lucky for you, you're almost as good of a sniper as you think you are. Pretty damn useful in the bedroom too." She rolled her eyes at his smug expression and turned to look out the window.

The mess was fairly busy at this time of the day cycle. There were quite a few people milling about and chatting, many of them glancing surreptitiously in the direction of the med bay. She turned back to Garrus. "I'm guessing the secret's out now, huh?"

"Yeah, uh… sorry about that," Garrus said, rubbing the back of his neck. She was sure he'd be blushing if he could. "I was worried and couldn't stay away."

There was a long pause before Shepard spoke again. "Seeing as I'm incapable of running away," she said, motioning to her IV line, "this is as good a time as any to say what you were going to the other day." She tried to smile at him, but the tension between them made the joke fall flat.

Garrus typed a command into his omni-tool, closing the shutters over the med bay windows. As he stood to pace, Shepard felt a cold feeling wash through her. Surely the IV line was feeding ice into her veins.

"Shepard, I, uh…" His hands fidgeted nervously. "I don't think I can stick to just easing tension with you." He avoided her eyes as he rushed to continue. "So if you'd rather end it, that's fine, I won't force you into anything." The turian looked flustered as the words tumbled out, running his talons anxiously over his fringe. "I mean, I couldn't force you anyways, but I just wanted to—"

"Garrus." Her hand snapped out and grabbed his arm as he paced past her bed. "Look at me." He met her gaze nervously, afraid and yearning. Her stomach fluttered, her heart raced, but she kept her voice slow and steady. "Garrus, are you trying to tell me that you want this to be more than just physical?"

The moment they gazed at each other in silence seemed to be the longest of Shepard's life. Those blue eyes, so inscrutable to her once, now seemed to overflow with emotions. His voice, when he spoke, was deep and hushed. "Yes."

Her face broke into a radiant smile. "Oh, thank god," she breathed. Her smile softened as she confessed, "I have no idea what I would have done if you said no."

His mandibles spread into a smile of his own as he moved to sit in the chair beside her bed. Shepard stopped him, quickly scooting over on her narrow hospital cot and shooting him a pleading look. Wordlessly he climbed on and wrapped his arms around her, tipping her back until she rested her head on his shoulder. Though Garrus didn't make the softest pillow, Shepard sighed in contentment. No matter how inconvenient their relationship, no matter how complicated, she knew there was nowhere she'd rather be. She lay against him in contented silence until she felt him shift behind her. The two of them almost had a sixth sense about each other, and that little shift was enough to tell her that he had something more to say.

"I'm sorry, Shepard," he said, and her head tipped up to look at him.

"For what?" she asked, taken off-guard by his words.

His words tumbled out in a rush. "I should have noticed something was wrong after the Cerberus attack. I should have realized before then that you needed hydration and rest. A turian should always be in tune with their mate's needs and I…" He trailed off at the odd expression on Shepard's face.

"Mate?" she repeated with a growing smirk. "We didn't do anything last night that I don't remember, did we? Because that would have rendered our little conversation just now completely unnecessary." She grinned at him disarmingly.

Garrus let out an uncomfortable laugh. "Not that I'm aware of. I, uh…" He paused, obviously flustered. "I don't think it translates properly. It's an old term, not official like a spouse or bondmate. I mean, there's a different word for couples who aren't dating seriously, but I think we just established that I am serious about you and…" He floundered, and Shepard couldn't help but smile. She really ought to help him out here, but his awkward stammering was adorable.

She finally took pity on him, laughter lingering in her eyes. "It's fine," she said, squeezing his hand. "You were busy doing what I asked you to do. I'd have been more upset with you if you'd ignored your duties in favor of worrying after me. Besides, neither of us were at our most observant last night. Need I remind you that I wasn't the only one who'd been drinking?" She smiled, and patted his hand where it rested around her waist. "And I think we just established that I'm pretty damn serious about you too."

Garrus's mandibles flared into a smile, and a low, happy hum vibrated in the air. Shepard's heart fluttered at the sound.

She hadn't had much patience in her life so far for men who attempted to 'protect' her. She'd bitten off Kaidan's head more than once for the offense. She preferred things the other way around—after all, it was the people she loved who always ended up getting hurt, not her. So why did his concerns fill her with a warm, happy feeling? Was it Garrus who was different, or was it her?

She liked to think it was him. She knew that he believed in her strength and abilities. He trusted her skills and judgment both on the battlefield and off. He worried because he cared, not because of some macho need to protect the little woman, like she'd seen too many times before. But perhaps it was she who had changed.

It had been only two years since she proved that she was not as invincible as she had believed, and it was he and the others who were forced to live on.

She knew, too well, what a burden that was to bear.

Shepard deliberately pushed such melancholy thoughts aside. She looked at Garrus. "Hey, big guy," she said, getting his attention. "A hundred credits to look the other way while I escape." She tried to look pitiable. It was harder than she expected.

Garrus gave her the turian equivalent of a snort. "I'm not going to cross the woman who passes out the pain meds, Shepard."

She shot him a look. "I'm starting to wonder who's really in charge of this vessel."

"Probably the one person who can actually give the captain orders."

"You're such a smug pain in the ass."

Garrus smirked. "Yeah, but you love that."

And damn it if he wasn't right. She absolutely did.

…