Running Silent:

Out of the Shadows

…

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.

…

"Liara, do you read me?" Shepard stood in the cockpit in full armor, a frown furrowing her brows.

"Yes, Shepard," came the asari's voice with audible relief. "Thank goodness you have arrived."

"I've got the base in sight," Shepard confirmed. "Things look quiet. I don't see any movement on the surface."

"That is because they are all inside," Liara said, exasperation in her voice. "Some of my guards are with me. Between them and the automated defenses, we have prevented the Cerberus teams from reaching the heart of the ship. But it has been a very close run thing."

"How do you recommend we board?" Shepard asked. "Same entry point as before?"

"Unfortunately I have no control of the docking bays at this time," Liara said dryly. "So I am afraid there is little other choice. I will transmit you the entry codes for the door."

EDI's scans of the Shadow Broker ship had revealed the Cerberus frigate docked directly to it. Armed with this information, Shepard knew that they had little choice but to disable the frigate from inside. They couldn't take the chance of damaging the Shadow Broker ship along with it.

"We'll be coming down in the shuttle," Shepard said. "Do you have schematics for the base?"

"Transmitting now," Liara said, sounding harried. "Please hurry, Shepard!"

"Just hang on, Liara," Shepard said, sounding as unruffled as ever. Only the worry in her eyes gave her away. She turned to Joker. "If that Cerberus ship leaves dock, blow it out of the sky."

"Aye aye, ma'am," he said with a nod.

Shepard met her team waiting in the cargo bay. All of them were suited up—she'd even gone so far as to request Kaidan come along. They both knew it was an olive branch, an attempt at making peace.

"Everyone on the shuttle," she said, taking the weapons that Tali and Garrus held out to her. "I'll make assignments en route. We don't have any time to lose."

"Take us in quietly," she said to Cortez, marking the entry point on his map. "As close to this location as possible."

"Yes ma'am," he said in his usual gentle tone.

Shepard turned back to the shuttle's hold, surveying her team. Most were looking at her, waiting for instruction. Tali looked worried, unable to hide her fears for her friend. Shepard saw a few tell-tale signs of worry in Garrus's expression as well, but he seemed focused, ready for battle.

"Tali," Shepard said, catching everyone's attention. "You'll be leading an infiltration team onto the Cerberus frigate. Solana and Kasumi will go with you. Your goal is to disable the ship in such a way that it can't escape or communicate. While I appreciate you eliminating any Cerberus troops in your way, that is not your main goal. Don't get sidetracked."

"Yes, Shepard," Tali said with a decisive nod, already looking more focused now that she had a job to complete.

"The rest of us are doing the opposite," Shepard said. "We're going to make as much noise as possible, drawing the Cerberus troops away and splitting their attention. We need to clear out the base."

Shepard turned back to Tali. "Comm Joker when you board the Cerberus ship. He has orders to blast it out of the sky if it tries to leave. I don't want to see you blasted with it."

"Coming in on the LZ, Commander," called Cortez from the cockpit. The shuttle door opened as he hovered over the ship's hull. They crept quietly to the door Shepard had remembered using previously to get into the Shadow Broker base. It seemed like such a long time ago now.

"A little too familiar, Shepard," Garrus said wryly, looking around for threats.

Shepard rolled her eyes as she used Liara's entry codes. "Try not to get knocked out by a desk this time."

Once they got inside, Zaeed started firing at the far end of the hall. At Shepard's incredulous look, he said, "What? You said you wanted to get their attention. Got any grenades?"

Shepard huffed and tapped her comm, directing Tali's team to move out. "We're inside, Liara. Got one team heading to secure their ship. The rest of us are going to try to get their attention, take some of the heat off of you. Where should we be headed?"

"They are making a concentrated effort to get inside the main server room, where my data is stored," Liara said. "If you head that direction, you will no doubt find them."

At that moment, some of the lights started turning on and off in sequence, moving down the hallway to their right. Shepard tilted her head. "Liara, is that you with the lights?"

"What are you talking about, Shepard? What lights?"

"Looks like someone is using the emergency lights to try and guide us." She began to raise her pistol, feeling watched.

Shepard heard Liara gasp through the comm. "I lost contact with Feron hours ago. It could be him directing you! He won't steer you wrong, Shepard," the asari said firmly.

"Are you sure it's him?" Shepard asked, brow furrowed.

"How can I be?" she said. "But it is something he would do."

Shepard sighed. "Alright. Everyone, follow the lights. Carefully." And they began moving cautiously down the hall.

…

Tali's team moved cautiously down a dim hallway, following the path they'd memorized from Liara's plans. It wasn't a difficult task, reaching the Cerberus ship and disabling it. But Tali's stomach was tied in knots.

Her track record of leading teams and running missions was nothing to be proud of. She lost control of her team on Freedom's Progress. Gotten nearly everyone killed on Haestrom. Had needed Garrus's help to keep the Migrant Fleet from going to war. She was sure if Solana or Kasumi had been on Shepard's team as long as she had, one of them would have been chosen.

Creeping down that dim hall, she vowed to herself not to let Shepard down. She tried not to think of how often she already had.

Tali held up a hand to stop the team when they heard footsteps ahead. She peered around a corner to see a single guard. A nod at Kasumi had the thief cloaking and moving ahead for a silent takedown. The soldier slid to the floor with a groan, his throat cut, as Kasumi materialized in front of them. This scenario repeated itself a couple more times, with Kasumi and Solana taking turns, as Tali felt more and more useless. When they reached the Cerberus ship's airlock, she let out a sigh of relief. Finally something she was good at! Tali moved in to hack the lock as the others guarded her back.

Tali snorted at how pathetic the encryption was. Cerberus hadn't refined it at all in the time since they'd left. This encryption was similar to what the Normandy's was before Tali had upgraded it, and sadly lacking EDI's active blocking measures. It took only a few minutes to break in. The door slid open to reveal an empty airlock.

"Joker, we're boarding the Cerberus frigate," Tali said softly into her comm.

"Copy that," he replied.

Tali motioned her team forward. The layout of the frigate was similar to the Normandy's, which made it easy to navigate. The airlock should open directly next to the cockpit. Another quick hack job made the door slide open. Solana and Kasumi cloaked and moved ahead as Tali stayed hidden. She heard a few grunts and some soft banging. When silence followed, she peeked out to see her teammates materializing over a few downed men in the CIC. She gave them an approving nod before turning towards the cockpit door. A third time they watched her back while waiting for her to finish hacking the door. The pilot and copilot were waiting for them.

The pilot had his sidearm up as the copilot spoke into her omni-tool.

"Intruders in the—" She didn't finish her thought before Kasumi's flashbang stunned them both. Tali fried the omni-tool, making the copilot scream at her painful electrical burns. Solana shot the pilot twice in the stomach as Tali finished off the copilot with her shotgun.

"Can you fry it?" Tali asked Kasumi, who was studying the control panel.

"A few pulled wires and a well-placed overload should put them out of commission for a few hours," she said with a shrug. "We don't need to do irreparable damage, do we?"

"We need the comms and flight console down long enough to finish the Cerberus crew," Tali said. "As long as they can't repair it before Shepard finishes clean-up, it's good enough."

They set to work destroying the comm systems and flight console, rendering the ship unable to fly or communicate for the time being. Then they headed back out into the CIC.

"If this ship's internal systems are like the Normandy's, we can take a maintenance shaft down to the main battery," Tali said quietly. "There should be an entrance through here." She motioned to the door that, on the Normandy, led to what was once Mordin's lab. "Weapons ready."

Solana raised her pistol, but Kasumi merely cloaked. This door was unlocked—Tali only had to press a button.

They found themselves unexpectedly in the armory. A single Cerberus soldier stood between them and the shaft. Before he could react, Kasumi's blade slit his throat. He fell to the ground, dead.

Tali moved ahead to open the hatch for the maintenance shaft. "Follow me," she said. "They can't have moved the main battery, at least."

Solana let out an irritated huff at the small size of the shaft. "Couldn't have designed this with turians in mind, could they?"

"Sorry," Tali said with a shrug. "It'll be a tight fit, but you'll make it through. Come on."

Tali led them through a maze of crawlspace, through tight tunnels that led past many of the ship's systems. She could think of a dozen more ways to sabotage the ship, but those would likely alert others of their presence. It was essential that they reach the main battery.

Solana let out a sigh of relief when they dropped down into the battery chamber. Tali's knowledge of ship maintenance came in handy as she knew just how to damage the firing mechanisms in small ways that would be catastrophic should they try to fire. Solana made her way to the main console and inserted a small drive.

"What is that?" Kasumi asked.

Solana chuckled. "A little virus Garrus gave me on the ride over. Even if they do manage to repair this ship enough to fire, their targeting parameters will be so far off they won't hit a thing."

"Nice work," Tali said as she came to join them. "We're finished here, so let's get out while we still can."

Solana sighed. "Back in the shaft?"

"Back in the shaft."

…

Liara was exhausted.

She sat against the wall, leaning her head back against the cool metal. The Cerberus troops would be back soon. She just needed a moment's rest…

"Buck up, kid," came her father's gravelly voice. "There's noises coming down the hall."

Liara stood on heavy legs, stretching and wiggling her fingers. Her biotics had been under such strain these past few days. But she would never give this up without a fight.

She stood at the ready, breathing slowly, preparing herself to fight.

"Liara! It's us." Shepard's voice rang out on her comm. "We've almost reached your location. Call off your people."

Her troops looked at her for confirmation and she waved them down. Liara sagged back against the wall again as Shepard came into view, though only Garrus was with her.

"Where are the others?" she asked.

"I sent Kaidan with a team to follow some Cerberus guys who seemed to be splitting off from the main group. We've cleared out a lot of them, but they must have squeezed a pretty large crew onto that frigate," Shepard said with a shake of her head. "It's going to take some time to be sure this place is empty."

"It doesn't matter," Liara said with certainty. "Cerberus knows the location. They can send people back whenever they want. I can't remain here." She pushed herself off the wall, trying not to waver where she stood. They had a long day ahead of them still. There was work to be done.

Shepard's brow furrowed. "Then what are you planning?"

"Empty the core. Remove the drives, everything I need for my network. Then find a new ship, something small and mobile."

Garrus's mandibles fluttered. "It won't be easy to find a ship in wartime," he reminded her.

Despite her exhaustion, Liara smiled. "Please, Garrus. Remember who you're talking to."

Shepard's comm buzzed. "We're on our way to you," came Kaidan's voice. "And we're bringing a friend."

Relief washed over Liara—it must be Feron. He was a survivor, but… well, she couldn't help fearing for him. Now she could focus on the problem at hand. Namely, how to get her equipment safely onto the Normandy.

"What do you want to do with this place when we've got everything you need off the ship?" Shepard asked.

Liara smiled. She had a plan for that.

…

It wasn't easy, getting all of Liara's equipment off the ship.

Garrus was glad he was overseeing the technical side of things rather than assigned to sneak the parts to the Normandy. It was, by far, the most cumbersome part of the plan. Everything had to be moved from the core all the way to the hatch they had used to enter. From there to the shuttle to the Normandy. And then the shuttle would come back for another load. As he understood it, everything was being set up in the observation lounge for now. It was practically the only open space left, except for Grunt's old room, and nobody really wanted to set up camp in there.

Garrus refocused himself—Liara would kill him if any of her information was missing or was damaged due to equipment being disconnected incorrectly. He just hoped they would be finished soon. He really didn't want to be responsible for a firefight among Liara's most treasured belongings.

…

It took hours to finish transferring everything over. There were a number of close calls during the process—Liara's eyes widened at a bullet hole in one of the computer casings. Luckily nothing essential had been damaged. It was inevitable that they would cross paths with Cerberus during their attempt to liberate the equipment.

Shepard was relieved when it was all over. She stood with Liara in what used to be the control room to discuss the next step. "How, exactly, do you plan to crash this thing into the planet core?"

"If we stop the engines, it will fall on its own," Liara said. "They are all that keeps the ship aloft."

"So are we shooting it down with the Normandy?" Shepard asked. "I'll have Garrus head back to the battery."

Liara shook her head. "I was planning to simply shut them down from inside."

Shepard put her hands on her hips. "From inside? Leaving yourself how much time to escape? That's a foolish plan and you know it, Liara!" Her voice was scathing. "There's too much unnecessary risk involved."

Liara shook her head. "This ship is sturdier than you think, and the engine is centrally placed. If we attack it from the Normandy it could take too long and the remaining Cerberus troops could realize what we're doing. Or they could send reinforcements!"

"Then let me be the one to shut down the engines," Shepard said. "We can't lose the shadow broker right now, Liara. Your information network could be central to winning this war."

Liara huffed. "And you think your life is worth any less than mine? Don't be ridiculous, Shepard!"

As the argument was beginning to heat up, they both turned at the sound of a throat clearing. Feron stood beside them. "I'll do it," he said firmly. Shepard blinked. Liara started to shake her head.

"Don't argue, Liara," he said. "I know this ship better than anyone, even you. I can shut down the engines and reach an escape pod in time. You know I can do it."

Liara looked anxious. "But if you don't—"

"Then the galaxy will keep on spinning," he said, cutting her off. "It's the best option. Now let's do it before we waste any more time."

Shepard nodded. "Good luck, Feron. We'll be waiting for your pod." She took Liara by the shoulder and the others followed.

Liara turned in Shepard's grip. "Feron—"

"Go, Liara," he said. And then he was gone.

…

Aethyta watched her daughter pace the cockpit. She hadn't know Liara cared so much about this drell. The last thing she wanted was for her kid to be going through this war with a broken heart. But these things couldn't be controlled. So she watched and waited, and hoped the drell would come through alright.

Commander Shepard stood with her hand on the pilot's shoulder, watching and waiting with them. She didn't move a muscle.

"Engines are stopped," the pilot said. "The ship's dropping."

"Do you see Feron's pod?" Liara asked urgently.

"Give him time," Shepard said, never taking her eyes off the viewport. "It'll take a minute."

Aethyta didn't look out the viewport. Her eyes were on her daughter.

And when pure relief washed over Liara's face, Aethyta felt it too. Liara was spared that grief… for now.

Liara left the cockpit to meet Feron in the docking bay. But Aethyta stayed and watched as her daughter's ship sank deeper and deeper into the cloud cover, sinking below the surface until it was a dark shadow that simply faded away.

Minutes later, a wave of bright purple energy pushed through the clouds, bursting out like rays of light. The mass effect engine had blown.

"It's done," Shepard said with finality, and turned. Switching gears, she said, "Joker, we need to rendezvous with Admiral Hackett about the Rachni. Head for the coordinates he provided."

She looked at Aethyta. "I believe Miranda has prepared sleeping arrangements for you, Liara, and the rest of her remaining crew. I'm heading to her office if you want to come with."

Aethyta shrugged, and followed. Hell of a day.

…

Shepard smiled when she saw Garrus waiting for her in her quarters.

"Long day?" he asked, with a touch of humor.

"The longest," she said as she walked into his arms. "Glad we got Liara out of there okay."

"And we even got the equipment," Garrus agreed. "It was a good day's work."

Shepard nodded against his chest. "Everyone's settled in, at least until Liara finds herself a new ship. She seems to think she can find one quickly, even in the middle of this war." She shrugged.

Garrus motioned to the table. "I brought some dinner up," he said. "I figured you probably forgot to eat with all that's going on."

Shepard laughed, moving towards the table. "You know me well, Garrus." She pressed a kiss to his mandible. "Thank you."

"Any time," he said.

Shortly after they had sat down to eat, they were interrupted by EDI.

"Commander," the AI said, "Tali is on her way up and appears to be in distress."

Shepard looked at Garrus, her brow furrowing. A moment later, the door opened and both of them shot to their feet.

"He promised!" Tali burst in, sobbing. Shepard ran to her, Garrus a moment behind.

"Legion promised! He swore they wouldn't," the distressed quarian continued.

Shepard felt a lead weight in her stomach. "What happened, Tali?" she asked, putting an arm around her younger friend.

Tali's helmet tilted upward and Shepard could see her tears through the tinted glass. "The geth attacked the fleet."

Wrapping both arms around Tali, Shepard locked eyes with Garrus over her shoulder. Something was very wrong here.

…