• Published 27th Jul 2013
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The Commander of Shepherds - pchn00



An amnesiac Commander Shepard has been living and thriving in the Everfree Forest for several months. Saving the life of a passing pegasus sets a chain of events in motion that could change Equestria forever.

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Chapter 19: Choices

Chapter 19: Choices

Noteworthy stood silently in the cargo hold eyes closed as instructed, ears perked and alert. At first she'd found the hum of the ship noisy and distracting but now she could only hear it if she really focused on it. Life had certainly taken an unexpected turn, she mused to herself.

The past week had been filled with noise, violence, and a lot of gooey alien blood. Some of it from the aliens at her side, but most from the aliens she aimed the plethora of weapons Commander Grunt had fastened to the armor they'd given her. She was bereft of both guns and armor, and was a feeling a bit naked without the comforting weight settled on her haunches.

She was told this was an important ceremony however and no matter where she was or what she did, Noteworthy was most certainly a pony who appreciated the importance of pomp and ceremony. Her eyes snapped open as the door to the hold hissed open, and the asari second in command of Grunt's unit entered. "The Commander is ready for you, Noteworthy. Are you sure you want to do this?"

Noteworthy regarded Veena silently for a moment. She and the asari had spent as much time together off the field as on. Once they learned mixing their magic and biotics resulted in an explosion equal to a small 'thermonuclear warhead' whatever that was, Grunt made sure to keep them close together at all times. Noteworthy had come to highly value Veena's friendship, her cool head on the battlefield and the interesting conversations they shared off.

"I'm sure, Lieutenant."

"Well then, right this way." Veena left, with Noteworthy trotting briskly at her side. "Don't be to nervous, we all had to do this."

Noteworthy nodded. She hadn't been told what officially joining Commander Grunt's unit consisted of, but she suspected the ceremony wasn't the sort one needed a gala dress for. She followed Veena out of the hold and into the crew mess, where it seemed the bulk of the Grunt's Grunts had gathered. The normally poorly disciplined crew of men and women were standing sharply at attention as the pair entered, with Commander Grunt himself at the head of the group.

Veena moved to take her place in the line with her squad mates, leaving Noteworthy to face down Grunt along the center. The towering krogan stalked up to her, looming above her and staring her down. "...someone get over here and lift her up."

Veena hastily moved to comply, gripping Noteworthy below her forelegs and holding her up so she was eye level with Grunt. The Commander cleared his throat. "Alright then. Noteworthy. You want in the squad?"

Noteworthy's eyes shifted from Grunt's to the assembled men and women in the room, all of whom stared ahead stoically. Then back to Grunt's, nodding firmly. "Yes, Commander."

"Alright then." Rearing back Grunt rammed his forehead solidly into Noteworthy's, eliciting a sharp CRACK. Several soldiers about the room flinched and winced, remembering their own inductions.

Grunt stared at Noteworthy in silence for a long moment.

Then one eye twitched.

Then he wobbled and almost dropped to a knee, drawing several gasps from his squad.

Veena's grip on Noteworthy tightened a bit in surprise. She knew the ponies were tough little bastards but they hadn't gotten around to doing anything approaching a proper test to gauge their actual thresh hold.

Sensing things hadn't gone quite as expected, a suddenly nervous Noteworthy squirmed in Veena's hands. "Should we um... do it again, sir?"

"No! ...no, no. Once was fine. Er... good. Good. Carry on. I'll be in my quarters. Don't bug me for a while." Grunt took a wobbly step away, then another. Before taking a deep breath to collect himself and try to get the world to stop spinning. It complied eventually and he was on his way to the elevator, only rocking slightly in place while waiting for it to arrive.

"We need to replace this damn thing."

***

Councillor Urdnot Wrex's private ship, The Urdnot's Hammer didn't so much fly through space as it almost seemed to push its way through. The massive vessel was more armor plating and weaponry than actual ship, and while very few would think attacking the thing a good idea it didn't exactly get where it was going at impressive speeds.

The ancient krogan reclined his favorite chair he found far comfier than he'd admit to anyone while reviewing the security footage from the Citadel fight for the umpteenth time. Finally he made a call. It took longer than he'd have liked for Grunt to pick up on the other line. The younger krogan holding an ice pack to his head. "What is it, old man?"

"Hmph. What happened to your head?"

"I don't wanna talk about it." By the way Grunt shifted his eyes away from the screen Wrex assumed he injured it doing something stupid. "You call for a reason?"

"I did. I think Shepard might be back."

To his surprise, Grunt just blinked slowly. "And?"

"And?! What d'you mean and?"

"And that's old news, I've known for a week now. Is that all you called to tell me?"

Wrex gnashed his teeth. "Are you fucking with me here, boy? Because I am not in the mood. How the hell do you know she's back? Aren't you curious how she survived this long?"

Grunt shrugged. "She fired the Crucible then rode the wave to uh... Equestria I think she called it. She shacked up with one of the royals there, because of course Shepard hopped into bed with the first alien woman she could. Collectors abducted her mate's sister, now Shepard's after them."

Wrex narrowed his eyes. "How do you know all this?"

"Oh uh, we picked up about a hundred of the natives when we raided a Collector ship. Dropped off most of em on Thessia. Just finished inducting one to the squad."

Wrex stared at Grunt for a long drawn out moment. Long enough for Grunt to fetch himself a bottle of rynchol and settle back at the terminal. Finally the older of the two let out a heavy sigh. "Alright. Fine. What are you doing now?"

"Mostly hunting Collectors. Trying to track down some kinda mega ship they have Note's Princess on."

Wrex settled back in his chair, brows knit together in focus. "I want you to rendezvous with me on Khaje. Shepard ran off with Javik and if that's really her we need to sit down and sort all this mess out."

Grunt seemed about to protest but closed his mouth, his own brow furrowing in thought. "Makes sense I guess. You think something big is going on then?"

The older krogan just stared hard at Grunt for a moment. "Something that looks, sounds, and moves like Shepard shows up on the Citadel with some sort of new alien species. Gets into a shoot out where the only casualties were a few ein, then steals the Normandy and rushes off into space. I think something's going on. She had that look."

"Heh. The 'get behind me and help or stay in front of me and get shot' look?"

"Yeah. And if she has that look..."

Grunt heaved a sigh and took a hefty pull off his rynchol. "It means we're probably fucked."

"Maybe. Maybe not. If that really is Shepard, I'm more worried about whoever's got her pissed off." Moving to sign off, Wrex paused. "Hey, how many of your crew have ein implants?"

Brows furrowed again, in confusion this time. "I dunno, not many of us. We don't have a lot of augments in the Grunts, mostly a couple omni-tools I think. Why?"

Fingers drummed on his desk, a sign the old krogan was thinking hard. "Swap em out for different models. I've had this funny feeling something's up with all this. A funny feeling I've been having more the further I get from the Citadel."

"Heh. Told you being around that dump isn't good for you. Should go home more. See the family."

"Bah! I see enough of my family. Half my crew and staff are my own kids. I'm serious about the implants."

Grunt shrugged. "Fine don't get your quad twisted. We'll set a course for Khaje. I think we're a couple hours from the nearest relay."

"Good. I'll probably beat you there. I'll try to keep you posted."

"Watch yourself out there old man. See you soon." Grunt signed off, settling back in his chair and removing the ice pack. "Implant removal, great." Heaving a sigh at the coming inconvenience he moved for the elevator when his personal intercom beeped. "What is it?"

"Sir we're picking up an N7 distress signal near Verin. It's garbled but clear, orders?"

"Well go pick them up! Then plot a course for the nearest relay, we're going to Khaje."

Grunt's disciplined crew knew better than to talk back when issued orders. A crisp 'yes sir' followed before the comm cut out. Heaving another sigh Grunt stepped onto the elevator, heading down to medical.

***

Lavish would be a very tame way to describe the accommodations Javik offered Twilight Sparkle and her companions. Not even the finest suites in Canterlot Castle came close to the opulent furnishings and foods offered the visiting group. While she wanted nothing more than to continue grilling Jack with an endless barrage of questions, she got the sense the woman was more interested in talking with Luna and Shepard than her. Plus...

"Hey, let's go check this place out! I bet these jellyfish guys have all kinds of crazy stuff to see."

AJ offered an affable shrug. "Sure, don't see why not."

Twilight was on her hooves quickly, moving to stand between her friends. "That's an excellent idea, I'm sure Javik can point us in the direction of some very interesting land marks and sights to see." She didn't notice the brief flash of disappointment on Rainbow's face, or the look of relief on Applejack's.

"Sounds like a mighty fine idea, we haven't had a lot of time to hang out together since leavin' Equestria anyhow."

Dash huffed and rolled her eyes. "Fine whatever, a guided tour. Sounds fun." She trotted briskly ahead of the pair and out the doors.

Twilight leveled a faint frown at Applejack. "Is she mad at me?"

"Nah, think the problem is with her not you, sugar cube. Reckon she's a mite frustrated about everything. Been a while since we couldn't shoot a rainbow at a big problem y'know?"

"Well what should we do?"

AJ shrugged. "Let her be. She'll sort herself out. Figure she'll do some flyin' an feel better after she clears her head. Been a while since she could stretch her wings."

"If you're sure." Twilight took a deep steadying breath. "Well! Let's go explore an alien planet."

Applejack chuckled softly. "Didn't think that'd stop soundin' crazy but here we are. Let's go see the alien water planet."

"Allow me to escort you then?" Elezzia moved up alongside the pair.

"Oh! Um, well of course that would be lovely." Twilight flashed a bright smile. "You don't want to stay here with your um, with Shepard?"

"Father. In our culture the one who gives birth is the mother, the other the father. Sometimes they prefer to both be called mother but by and large it's as I said."

"Oh how interesting. You know I have a lot of questions about asari..."

Applejack sighed and rolled her eyes. She followed after the chatting pair, wondering how far ahead Rainbow Dash had gotten.

***

Luna ran her fingers along the rim of the glass she'd been sipping for the last half hour. She'd come to this tavern, a bar Shepard had called it, with her, Jack, and Javik. Shepard and Javik were conversing quietly at the other end of the bar, leaving Luna alone with Jack. She knew she shouldn't be intimidated by Jack, but the woman had a very real aura of danger about her that put Luna on edge. She was far older and more skilled with her magic but even so...

She nearly leapt out of her seat when Jack abruptly shifted focus from Shepard to her. "What happened to Shepard? For real?"

Luna blinked taken aback by the abrupt question and not entirely sure what she was being asked. "What do you mean? Did she not relay what occurred?"

Jack rolled her eyes. "Yeah but she's an idiot woman child. She's different, very different."

Luna looked over Jack's shoulder at Shepard, the woman gesturing emphatically with a huge grin on her face while Javik wore a barely noticeable smile of his own. "I'm afraid I only know this Eliza. Not the one you traveled with."

"Eliza." Jack let the name roll off her tongue and frowned faintly. "You know I didn't even know her first name til they threw up that shitty museum? One of a lot of regrets I had."

"Had?"

"Mmm." Jack's eyes drifted to her own glass. "It's weird how time changes someone. I grew up a lot between blowing up the bug hive and the war on Earth. Grew even more after it. I still can't wrap my head around the years. But I check in with old buddies now and then. Grunt and Javik mostly. Everyone else is dead. I miss 'em all. Even the cheerleader." She lifted her eyes to Luna's again. "You're some kind of immortal right? How do you handle it?"

"It? Losing friends and loved ones I assume?" At Jack's nod she continued. "Well I hate to give an unsatisfying answer but I've never had to endure such a loss. My parents were gone before I was old enough to remember them and I worked very hard to keep everypony at a far enough distance I never formed any attachments beyond my sister."

"Shit. That is unsatisfying."

Luna chuckled at Jack's frankness. "I apologize. Were it my sister I'm sure she'd have no end of ages old wisdom for you, alas I am far less accomplished and learned than she."

"I dunno, you seem smart enough. And you're not the one abducted by the bugs so you're probly more accomplished than you give yourself credit for."

Again Luna had to laugh. "Trust me, you'll see how accomplished my sister is when we free her from the clutches of these collectors. I wager you'll never see anything quite so spectacular again when she unleashes her fury."

"Hm. So hey, is it true you really move the moon around? How's that work with the tides and everything? Does the rest of the world just deal with your schedule of seasons and shit?"

"Ah! A fair question. You see-"

***

"Are you going to say anything or just stare at me?" SADI didn't look up from the displays when she addressed Valin.

The salarian started in mild surprise at being addressed. "Apologies. Didn't want to disturb you. Simply fascinated by functioning AI. Unheard of in our age."

SADI swiveled her chair around to face Valin, who was standing in the entrance to the cockpit. "If you have questions I'm happy to chat. I'm not doing anything terribly important."

"I see. What are you doing?" Valin took the invitation to sit in the co-pilot's seat next to her.

"Since entering hanar space I've detected an odd... signal. Signal is the best word for it, though no instrumentation is picking it up."

"Curious. Detected it how?"

SADI shrugged. Valin had to marvel at the very human way her brows furrowed and lips pursed in frustration. This was a real synthetic being right in front of him. Not some cheap VI. "I... this will sound foolish to a man of science."

"Met new species of equinoid alien capable of altering shape at will. Possibly met Commander Shepard in the flesh. Am keeping an exceedingly open mind today."

"Heh, fair points. Alright. I feel it, here." SADI tapped her chest.

Valin blinked. "Some sort of sensor array located in the chest?"

"I wish, no that would make sense. No just... I feel it. In my... I don't know."

"Heart?"

"I don't have a heart, Dr. Solus."

Valin shrugged quickly. "Soul then. Whatever idiom most comfortable with."

"I don't believe in souls."

Another shrug. "Stick with heart then or come up with own term."

"My heart then. I feel something in my heart. Telling me to follow it."

"Highly intrigued. Possible location?"

SADI tapped her chin in thought before standing and walking to the galaxy map. With a light tap she opened it. "Here. Right here."

"Hm. Less than an hour travel. One moment." Valin stepped aside opening a channel on his omni-tool. "Commander. Permission to depart for a few hours with synthetic SADI?"

"Granted. I'm not your Commander anymore Va-" Valin cut her off mid sentence. "Come along. Borrow a ship from the Hanar. Have plenty, don't use them." At SADI's unsure look he tilted his head. "Normandy upgrades will be at least twelve hours. Signal less than an hour out. Be back well before finished."

"Why are you doing this?"

"Why? Wildly curious. Have to know more, might go insane if we don't investigate immediately. Coming?"

SADI nodded and hastily jogged off the boarding ramp after the quickly departing salarian.

****

Javik held up a hand to quite Shepard as one of the Hanar drifted closer. "Deepest apologies for interrupting most honored enkindler."

"Yes yes, what is wrong?"

"A krogan warship is demanding clearance to land. It's designation is Urdnot's Hammer."

Shepard snorted in amusement, but Javik looked anything but. "Is Councillor Urdnot present?"

"He is, most honored enkindler."

Javik motioned for Shepard to follow. The woman glanced over her shoulder at Jack and Luna, the two deep in conversation before following after him with a shrug. The two along with their hanar escort left the main floor of the bar entering a private office. "Open a private channel to Wrex's ship."

If Javik was bothered by the owner of the bar currently occupying the office it didn't show. By the way he silently drifted from the office Shepard had a feeling this sort of thing happened often. Their hanar escort did as requested, and Wrex's scowling visage appeared on the terminal screen. "I'm coming down."

Javik frowned. "You may come down. Alone. Leave your flying junk heap in orbit."

Wrex glanced passed Javik to the silent Shepard. "Fine. Send coordinates for the LZ. And make sure that is with you too." With that he abruptly cut the feed.

"...should I be insulted?"

"Probably, he did call you a 'that'. Come along, let us go meet your volatile krogan."

"He's not my krogan but... probably a good idea, yeah." The pair left without another word to the hanar who silently closed the door after they left.

Crossing back through the bar Shepard made a warding motion to both Jack and Luna who were watching them curiously. She followed Javik out of the establishment and to one of the elevators to the surface. "What do you think this is all about?"

"Reapers, I have a passing suspicion."

Javik didn't miss the way Shepard went pale. Or the sudden twitch in her trigger finger. "That's not funny."

"No, it is not. Neither am I."

The room suddenly felt like it was spinning. Like all the air was being sucked out of it. Shepard felt herself swaying and she staggered back against the wall of the elevator. Her breath starting to come in short gasps. When she bumped the wall she jumped forward and whipped around, bringing her side arm out of her hip holster shakily aiming it at her own reflection.

Javik crossed the elevator in two quick steps putting a hand on both of the dangerous woman's shoulders.

Suddenly Shepard was somewhere else. She was in some kind of chamber as the lid was opening. Looking up she saw... herself. Herself and Liara looking down. She felt confusion, fear, anger.

The scene shifted. She was in the Normandy, talking to someone. To herself. Many conversations flashed by. The fear, confusion, and anger remained. But as the talks went on they eased, they were still there but... less so. Comaraderie, hope, righteous fury was taking the place of the negative feelings.

With a gasp she was back in the elevator. Slowly she lowered her gun and turned to look at Javik. "I was once lost as well, Commander. I know what it is you feel, what you are going through. If I thought you would listen I would tell you to remain here while we handled matters. But you would not, and you may endanger others by blundering in without supervision. So I will supervise you. I am... here for you, Shepard."

"I kind of want a hug, Javik."

Javik took one large step back and shook his head in mock disgust. "What did they do to you on that world?"

"I think they reminded me what it feels like to be human."

"Ironic." The elevator came to a stop and hissed open revealing the open sky of Khaje. "Maybe he'll give you one."

Shepard looked passed him to see Wrex, standing with his arms crossed. No visible weapons but she remembered he packed a mean biotic punch back in the day. She had a feeling that hadn't changed. When Javik made no move to go closer she took the initiative and started toward him.

She stopped as he surged forward. Nervously a hand moved to her hip where she'd holstered her pistol, but he stopped nearly nose to nose with her, glaring into her eyes with his large red ones. "...are you really her?"

Swallowing her nerves she offered a small smirk. "I'm Commander Shepard, and you're my favorite krogan on the Citadel."

Wrex's eyes widened a moment taking in what she'd just said. Then he laughed, a deep belly laugh that shook his whole body before scooping her into a crushing embrace. "I don't know if you're a clone and right now I don't care, but damn is it good to hear your stupid voice again."

Shepard gasped a little, legs kicking feebly against Wrex's massive arms. Javik just smirked as he approached the pair. "There, you got your hug. Feel better?"

She did.

****

Shepard sat with Wrex aboard his shuttle, just grinning happily listening to the old krogan ramble about family, the citadel, work, Tuchanka, everything. They talked for hours, into the evening. Javik left the two alone to oversee work on the Normandy and give the two old friends some privacy.

"Congratulations by the way."

Shepard tilted her head. "For what?"

"Your kid. She's just like you."

"Oh, heh. Yeah thanks... I'm starting to pick up on all that. I heard about your son, I'm sorry Wrex."

Wrex shrugged. "Wasn't the first one I lost. Still hurt like hell though. Your girl got it worse than me I think. They grew up together, they were on their retirement slash honeymoon cruise. When we get this mess sorted out I'll take you out for a drink and a cigar or something to celebrate you being a dad."

Shepard sighed and settled back in her seat. "Javik mentioned the uh... the reapers."

"Hrm. I think the ein are reapers."

"Helluva lot smaller than they used to be. How is that possible?"

Wrex shrugged. "I look like a science guy? They possessed people before right? Maybe they did that and didn't leave."

Shepard opened her mouth, then closed it. It seemed simple. An obvious solution and way to escape the destruction of synthetic life. "So what? Everything we did was for nothing?"

"What? Don't be stupid. Er. Stupider. It's been three hundred years and we're still here. I don't know what they're up to but I think the ein tech implants are involved. Grunt's crew is on their way, all taken their implants out. So has every krogan in the galaxy by now I think. Usually when I say something they all snap to it."

"Urdnot Wrex, most respectable krogan in the galaxy."

"Ha! You joke but you're not far off." Wrex grunted softly and rubbed his chest. "I think we need to sort this out now before it..." He grunted again, rubbing at his chest.

"Wrex?" Shepard was on her feet approaching.

"It's... nnnngh..." Wrex tried to stand and slipped, crashing to the floor of his shuttle.

"Wrex!" Lunging toward him Shepard suddenly found herself hoisted off her feet and slammed into the wall of the shuttle pinned by a biotic field.

"He'll recover, in time. I crushed several of his hearts to ensure he's properly incapacitated."

Shepard turned a furious glare at the entrance to the shuttle as Liara stepped aboard, one hand out holding Shepard against the wall. "What the hell do you think you're doing, Liara?!"

"Keeping galactic peace, Shepard. We've enjoyed centuries of it and I intend to make sure that doesn't end."

Shepard gritted her teeth as she felt the biotic field around her tighten, the woman squirming in pain. She noted Wrex's labored attempts to rise, before he slumped back to the ground and began to tap at his omni-tool. "Liara... gnn... we think those ein are the reapers!"

Liara sighed, never loosening her grip on Shepard. "Of course they're the reapers... whatever you are. Maybe you really are Shepard. If so that makes this all the more necessary."

The shock and confusion was clear on Shepard's face, prompting a sigh from Liara. "I've been the Shadow Broker for centuries, long before I became the asari councilor. I've seen the worst the galaxy has to offer every day for over three hundred years now. Yes, the Ein are the reapers in a new form but they no longer wish to wipe out all organic life. Just control it."

Shepard's attempts to escape weren't lessening, just intensifying. Liara wiped a bead of sweat from her forehead as she tightened her biotic grip further. It was just the strain of keeping the powerfully augmented woman pinned that was causing her knees to shake ever so slightly. Certainly not the look in the other woman's eyes as she glared down at Liara.

"Goddess... you really are Shepard aren't you? At first I dreamed of this. A miraculous reunion, you swaggering in with a smirk and some sort of asinine quip." For just a moment her grip began to ease, some of the hardness left her expression. Then she took a deep breath and tightened it again. "But that was a long time ago. I know what will happen if I don't kill you here."

Shepard's brief hope for escape vanished as quickly as it'd arrived as the biotic fields tightened around her even further. Air was coming in short supply and her vision was getting hazy. She was more and more aware of a pounding sound in her ears. Liara's voice was fading away, before it was abruptly replaced by a tremendous roar.

Wrex surged to his feet with a bellow, head lowered as he kicked into a charge. "You crazy blue bitch! I knew you were losing it but I didn't see how much!"

Without dropping the hand holding Shepard, Liara lifted her free arm in Wrex's direction. "I didn't want to do this, your loss will destablizie the krogan." Liara tightened her free hand and Wrex's charge staggered to a stop as he toppled onto his side.

He was dead before he hit the floor.

"Now for..." The murderous asari trailed off as she turned her attention back to Shepard. The woman's eyes were no longer the smoldering emerald green. Rather two pools of silvery light seemed to burn holes straight through Liara's soul. She was forced to swing both hands up in a renewed attempt to hold Shepard back.

She might as well have been trying to hold back the oceans of Khaje.

The explosion of released power ripped the shuttle to pieces scattering them all about the landing dock. Hanar and drell workers scrambled to get clear as Shepard's crew lead by Javik were charging toward the site of the explosion.

A battered and bloodied Liara looked up into Shepard's furious visage. She couldn't be sure but it almost seemed like the faint outlines of wings were visible behind Shepard. Of more immediate concern was the pistol leveled at her forehead, the barrel resting right between her eyes.

Author's Note:

Going to do something a little different for this one. You the readers will get to decide what happens next! One big problem I've had with this story is paralyzed with indecision so I'm fixing that by putting the decision in your hands.

Polling is closed, new chapter will ideally be out sometime next week!

Thanks for reading, and for sticking with me for so long. Hopefully not much more of a wait til we're done.