Running Silent:

Eye of the Storm

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.

In the relay's tunnel, everything was quiet.

"EDI?" Shepard called.

"Shields holding at seventy-five percent."

"Brace for deceleration," Joker said quietly, his voice as tight as a bowstring.

The realm of space that opened up in front of them looked no different than any other, but in the cockpit, silence fell. No living being had traveled through this system or seen this relay in at least fifty thousand years. As Joker piloted them into the system, towards an unnamed star, Shepard allowed herself a moment to stare in awe.

"Shepard…" Miranda's hand curled tight on Shepard's gauntlet. "Where the hell are we?"

Staring out into the abyss, she said, "Somewhere new."

Miranda's eyes drifted back towards the windows, too shocked to offer any protests.

EDI was the first to finally break the silence, and even she sounded regretful. "Commander Shepard, the relay is active."

"Acknowledged," Shepard said, pushing thoughts of beauty and discovery from her mind. They had a job to do. "Joker, get us as far as you can as fast as you can."

On the monitor Shepard watched the relay, dark until a few minutes before, brighten and spin with the arrival of another. Harbinger had followed.

The quiet that had filled the cockpit was a thing of the past. EDI and Joker called back status updates and warnings. Shepard shouted into her comm at Garrus to fire. Miranda stood still, her fingers in an iron grip around Shepard's arm, and asked for orders.

"We need to evade until we can lose him," she said, steadying herself when Joker made a hard turn.

"Reaper beam priming," EDI alerted them.

"Right in the firing chamber, Vakarian!"

"Brace yourselves!"

The Normandy jolted to the side, knocking Shepard out of balance. She stumbled, slamming her shoulder into the wall. She gasped as the pain burst forth; she'd forgotten her previous injuries. Menae seemed like a lifetime ago.

Shepard righted herself with her good arm, ignoring Miranda's pointed gaze at her injured shoulder. "Report," she ordered, breathless.

"Secondary beam glanced off our shields," Joker said, his hands still racing across the console.

"What's the status of our shields?"

"Shields are at sixty-five percent, Commander," EDI said. "However, they will not hold under continuous fire. A direct hit could disable them. I recommend—"

"I hate to interrupt EDI's little monologue, but the reaper's powering up again," Joker interjected. "Try to hang on this time, Commander."

Shepard clung to the navigator's chair as Joker executed a series of moves that Shepard hadn't realized the Normandy was capable of. The ship's inertial dampeners, lighter in the cockpit than in the central parts of the ship, strained under the pilot's demands.

"Hell yes!" Joker crowed in victory. "Missed us that time, you bastard!"

Shepard shook her head. She'd known he was the best pilot in the Alliance, but she'd never seen him at work before—not like this. "When we get back, I'm giving you a medal."

"If we don't all get arrested first," Miranda said dryly.

"Reaper beam priming," EDI stated. "Harbinger is gaining ground."

Shepard turned to her pilot. "Joker?"

"Doing what I can, Shepard." His voice was strained. Shepard felt the vibration of the thanix cannon under her feet.

Shepard tightened her grip as the Normandy evaded the beam, her eyes jumping between Joker's flying fingers and the space outside the cockpit windows. It was a dizzying view. The nearest planet dipped in and out of sight as Joker dodged the reaper's fiery beam. Sometimes she would catch sight of those red beams of light for a split second before they disappeared.

Shepard's hands were ripped from the navigator's chair by a violent shudder. She was thrown to the ground as the cockpit's lights flickered, slamming her head on the metal floor. Alarms and flashing lights blared on the console. "Shit!" Joker cried, pressing buttons faster than she could follow his hands. "A direct fucking hit. Shit!"

Shepard pried herself off the floor as quickly as she could manage, wincing at the intensifying ache in her head and shoulder. "Shields?" she barked.

"Five percent," said EDI.

Shepard paced the cockpit, fingers clenching into fists. "Shit."

"No more hits," Joker said. "I'm taking her into the gas giant."

"What?" Shepard demanded. "Are you trying to get us killed?"

"The Normandy can't take another hit, Commander! It's the only way to lose Harbinger."

Shepard trusted Joker with the fate of the galaxy. She could trust him with this. "Alright, Joker," she said, taking a deep breath to calm her nerves. "Do it." The planet loomed larger and larger before them as the Normandy headed directly towards it at full speed.

"Jesus," Shepard muttered, running a trembling hand through her hair. "This is the craziest thing I've done today, and I've set the bar really fucking high."

They were moments from reaching the planet when EDI spoke. "The reaper beam is priming."

The pilot was laser focused. "I can make it."

"Joker?" Shepard asked warningly.

"I can make it."

Swirling clouds filled their vision, surrounded them, and the Normandy gave a single, vicious shake.

"Was that a hit?" Shepard asked tersely.

"Negative," EDI told her. "That was our entry into the upper cloud layer."

Shepard stared out the cockpit windows, obscured entirely by clouds. "And Harbinger?"

"Harbinger has followed us into the gas giant," EDI said calmly. "Jeff, I suggest altering course. Our current trajectory has a high probability of death. I anticipate interception by Harbinger within two minutes and reaching crush depth within four."

"I was planning on it, EDI." Joker rolled his eyes, muttering, "Thinks she's my mom…"

A tremor went through the ship. "What was that?" Shepard asked. "Do we have damage?"

"Wind gusts," Joker explained. "The deeper we go, the stronger they're going to get."

"Then what the hell are you doing?" Shepard asked, feeling another shake under her feet.

Joker gave an exasperated sigh. "Look, Commander, Harbinger's going to be searching for us. The deeper in we go, the closer he'll need to be to get us in sensor range. I don't know about you, but I'd rather deal with a little chop than end up fried by a reaper beam."

Shepard looked up at a harsh creak from the bulkhead. "EDI?" she called, suspicious. "Exactly how close are we to crush depth?"

"Relax, Shepard," Joker interrupted. A tremor shook them. "I've got it under control."

Her ship had passed illegally through a relay, was inside a gas giant, and was being chased by a reaper. Relaxing was not on the agenda.

"I trust you, Joker," she finally said, then turned to the cockpit's resident AI. "What's the damage, EDI?"

EDI's blue orb blinked. "The shield generator sustained damage from the reaper's beam, Commander. Without making repairs, the shields will not return to full strength. The Normandy's armor also received minor damage in some areas. Additionally, the drive core needs to be vented soon. The Normandy was not designed to remain in stealth during long stretches of ship-to-ship combat."

Shepard took in a slow breath, pinching the bridge of her nose. Discharging the drive core would be a death sentence in the middle of their cat-and-mouse game with Harbinger. "What's your recommendation, EDI?"

"I suggest repairing the shield generator before leaving the planet's atmosphere. Placing the Normandy on emergency power during this time should allow for a longer period before the drive core reaches critical levels. If we are fortunate, Harbinger will call off his search."

Shepard cracked a smile. "Are we ever 'fortunate'?"

"If our current luck holds, there is a high probability that we will survive with a minimum of two close calls," EDI said. She paused. "That was a joke."

Shepard huffed a laugh. "Of course it was." She took a deep breath. "Alright, people. Looks like we've got a plan. EDI, drop us down to emergency power. Joker, keep the ship as steady as you can. Miranda, call up an immediate team meeting in the conference room. We're going to get those repairs underway, and we're going to get the hell out of here before Harbinger finds our hiding place."

Miranda gave her a rare salute as she turned to leave the cockpit.

Shepard glanced over to her pilot. "I doubt I need to tell you this, but I want you listening in on that team meeting, Joker."

"So, the usual." Joker tugged the bill of his SR-2 cap. "Got it."

"Switching to emergency power," EDI announced, just before the lights dimmed.

Shepard strode out into the CIC and paused at the top of the steps. Instead of ready at their stations, her crew was clustered in fearful whispers and worry. "Everyone to your stations," she ordered, keeping her voice calm and even. "I need you at the ready. Business as usual until I say otherwise."

The crew was quick to follow her orders, some of them visibly relaxing at the evenness of her tone. She nodded greetings at them as she passed, heading through Mordin's darkened lab on her way to the comm room.

The red emergency lighting in the empty room did nothing to minimize the ominous feeling of the ship's strained creaks and tremors. She caught herself on the conference table as an unexpectedly powerful shake made her stumble. She wound around to the head of the table, bracing herself against it as she thought through their situation. As long as Harbinger didn't find them, there should be no problem finishing the repairs in a timely manner. What worried her was what might come after. How long would Harbinger continue to search for them? How long could they last?

They were up shit creek with a very battered paddle, and though that wasn't unusual for the Normandy crew, she couldn't forget that she still had the primarch of Palaven and three of his men below decks. Great first impression, Commander, she inwardly groaned. Fucking fantastic.

After a brief reassurance and the parsing out of assignments, the team left the meeting just as tense as they'd arrived. Garrus made no move to follow. Shepard shot him an inquisitive look.

He shrugged, a bit too casually. "Just making sure you find your way to the med bay."

She motioned for him to walk with her. "I will if there's time. First, I need to go smooth things over with Victus." She could feel him tense beside her, but he didn't say anything until the elevator doors closed behind them.

"Shepard, I saw you get injured down there. Your shoulder and back need to be looked at… as does your head." He frowned. "When did you manage that?"

She reached back, wincing as her fingers came away with a small amount of blood. "Damn," she said tiredly. "I guess bouncing around the cockpit wasn't my best idea."

"So you'll go to the med bay," he said with finality.

She huffed. "Go to hell, Vakarian."

He put his hand on her back to guide her through the open elevator doors. "Yes, ma'am," he said, "as soon as you go to the med bay."

She stopped short in the hallway and spun around, her jaw firmly set. Garrus sighed. "Look, let me smooth things over with Victus. I've met him before, and—while he's no xenophobe—I think it might be better coming from another turian. I can also ease some of his worries about you. When this is all over, then you can have your chat."

Shepard glanced at the door to Starboard Observation and then back at her turian mate, unable to refute his logic. "Alright," she relented. "If you think that's best. Let me know how it goes."

"Of course, Commander," he said, heading towards the med bay.

"Uh, Garrus?" She raised her brows at him. "I think Victus is that way." She inclined her head towards the observation deck door.

He smirked. "Wouldn't want you getting lost on the way to the med bay."

She rolled her eyes. "Of course not." Accordingly, he didn't leave her side until he was assured that she was in the doctor's capable hands.

Chakwas clucked over Shepard like a mother hen as she stripped away her armor to reveal her wounds. Shepard winced at the sight of her damaged hardsuit, mentally cataloguing what she could repair and what would need to be replaced. At first Chakwas lectured, but she soon fell quiet in concentration, her work complicated by the tremors that still shook the ship. All that filled the silence were the ship's creaks, groans, and shudders, interrupted by the occasional clink of the doctor's tools.

Quiet, as every soldier knew, did not mean peace. It was only the calm before the storm.

While Shepard sat insulated in the med bay, the Normandy was fighting for her life, racing against the clock and against a powerful enemy in order to survive. Their odds weren't favorable, but Shepard didn't care for hearing the odds. She knew what she and her crew were capable of.

"All finished, Commander," Chakwas said finally, snapping the gloves off her hands. "Try to be careful next time, will you?"

"No promises," she said, grinning at the doctor's sigh as the doors closed behind her. Shepard glanced at Starboard Observation as she made her way to the elevator and wondered if Garrus was still inside. Despite the temptation to check for herself, she instead took the elevator down to engineering to look in on the repairs.

Joker turned in his chair as Shepard strode into the cockpit. "All systems go, Commander. Ready to make our daring escape?"

"Ready as I'll ever be," she said. "How are we looking EDI? Has Harbinger made an appearance?"

"He has passed within scanning range but never close enough to incite alarm. It has been twenty-two minutes since he was last on my scanners. It is possible that he has ended his search."

"I wouldn't count on it," Shepard said, "but I think this is our best bet to escape either way." She put her hands behind her back. "Take us to the relay, Joker."

He spun back to the dashboard, hands at the ready. "Aye aye, ma'am."

He took them out of the gas giant slow and quiet, keeping a close eye on their scanners. Nothing seemed amiss, but Shepard stood at attention, ready for anything.

Her omni-tool lit up in the dim cockpit, bright and unexpected.

"Shepard." The ship vibrated with his voice.

Had she not been so thoroughly trained as a soldier, Shepard would have jumped at the intrusion of Harbinger's sudden, deafening voice. On her ship. On her comm. Her body tensed, rage-filled and combat ready.

"You only fight the inevitable."

Shepard's stomach turned. No, it wasn't just her omni-tool. It was every speaker on the whole goddamn ship.

"Joker?" Her voice vibrated with urgency.

He jerked out of a shocked stupor, fingers flashing across the keys. "He's blasting through on every frequency!" the pilot cried. "Every radio in the whole damn system is—"

"You may run. You may hide. But your time is wasted."

"EDI?" Shepard cried. Nothing.

"The harvest will continue, but you will not. I will find you… Shepard."

Silence fell, and all was still. Shepard barely dared to breathe, her mind racing in fear and worry.

"I have regained control," came a sudden, welcome voice.

Shepard breathed a sigh of relief, but a crease was permanently etched between her brows. "EDI. What happened?" She began to pace.

"Harbinger's signal was too strong for me to overpower," she explained.

Shepard paused in her paces. "There's no way to block the signal?"

"Harbinger used brute force to break through on every frequency," the AI explained. "Trying to block the signal would be akin to encrypting a locked door to prevent entry by explosives."

"Christ," Shepard muttered. "Can you imagine what they're doing with this on Earth?" She closed her eyes and drew in a deep breath.

"Commander?"

"Yes, EDI?" she replied, squeezing the bridge of her nose.

"I suggest urgency. It appears Harbinger has used the signal to locate us."

Shepard's head shot up, eyes burning in anger. "Gun it, Joker," she barked. "Get us the fuck out of here. Now."

Joker's hands raced over the console even as he protested. "How do you even know?" he demanded of the AI. "He's not even on—"

A new blip on the scanner cut him off.

"Shit."

"Aren't we still stealthed?" Shepard asked, pacing across the cockpit. "We're in motion. He won't know our route now that he's stopped broadcasting."

Joker scoffed. "Where else would we be headed but the relay, Commander?"

"Harbinger is closing the gap," EDI helpfully interjected.

Shepard glanced at the scanner. "Joker?"

"We'll make it," he argued, never taking his eyes off the console. "Have a little faith, Commander."

The relay loomed steadily closer. The blip on the radar did the same.

"Harbinger will enter firing range within forty-five seconds," EDI told them.

"Yeah, I know, EDI!" Joker scowled. "Will you just shut up already?"

Shepard gripped the pilot's head rest, feeling a sense of deja vu.

"Engaging relay," Joker finally announced. "Jumping in three, two, one…"