Chapter Text
The first anomaly occurred six months before Commander Shepard was set to be awoken, and only three months before she actually did wake up for the final time.
Brain activity had been steady - that is to say, almost nonexistent - up to this point, as was expected. It was on that day that several localized shocks and hormone injections would reawaken the Commander’s higher brain functions and return her to actual life, rather than the brain dead vegetative state her body had been in for the last few months.
The procedure went well. Scans indicated that her higher brain functions had returned, well beyond optimal parameters and entering the “overly optimistic range.” Miranda was pleased. It would seem her attention to detail and consistent hyper management of her underlings had paid off.
They’d done the impossible. They’d resurrected the dead.
The thing is, Shepard wasn’t supposed to wake up, and she definitely wasn’t supposed to wake up screaming. The sound took the celebrating scientists and doctors by surprise, and they all stood there, mouths agape like idiotic fish. Absently, Miranda noted that the brainwave monitors must have malfunctioned, because no human brain should be able to return readings like that.
“Get a sedative, now!” She snapped at the nearest doctor, and the sharp command broke them out of their shocked stupor. Doctor Henries hurried to follow her order, all of them flinching and cursing when Shepard thrashed on the operating table, one arm coming free of the restraints they thought redundant. The Commander’s back arched up off the table, the skin around her multitudinous glowing cybernetics - which hadn’t even begun to heal - tearing viciously.
Henries rushed to Shepard’s side, Miranda alongside to help hold her down with biotic enhanced strength, but the moment they touched her, her cybernetics pulsed, and a corona of biotic flame and crackling lightning burst into existence around her in a flash of crimson. The surgical table bent, groaning and shrieking as it melted/de-atomized, while blood-red lightning arced out from the Commander, scoring across the ceiling and walls, bursting lights and exploding the thick glass wall cordoning off the observation room.
Henries shouted something, his words swallowed by the hum of biotics and the sound of thunder, overwhelmed by Shepard’s own agonized cries, and made to drive the sedative home in Shepard’s neck.
Her arm lashed out, breaking out of Miranda’s grip, awash in crimson fire, and then Henries simply didn’t exist anymore; erased by a warp field so strong all it left behind were his shoes and a few hairs that floated aimlessly through the now rippling space he once occupied.
Before Miranda could grasp what had happened, that same hand flashed forward, seizing her by the throat and dragging her down, down, until she was face to face with Commander Shepard herself. A face that was more open scar tissue than face at that point. Cybernetics were plainly visible across her brow and lining her cheekbones, drilled into her temples and fusing her shattered skull back together, and the tissue that would eventually make up her lips and cheeks simply hadn’t grown back yet. The sight of her had never unsettled Miranda until then, until she saw the macabre, cybernetic skeleton half dressed in muscles and skin move.
The Commander’s eyes were open and bleeding - they weren’t ready, the cybernetics hadn’t fully taken yet and they glowed unnaturally, the same blood-red color as her biotics - and all she saw there was rage and pain the likes of which she could scarce begin to comprehend.
And then she spoke, and her voice echoed, not in the room but in Miranda’s mind, and it was a thunderous thing that would have driven the genetically perfect human to her knees if Shepard were not holding her up by her throat.
“ You should have left me dead! ”
It was only later that Miranda learned that it was Jacob Taylor who managed to inject the Commander with a sedative, before the energy field she was emitting shredded them all down to their last atom. In the moment, it was all she could do to keep hold of the air of compunction that she had always maintained, and get the doctors and surgeons working on the next round of treatments immediately!
“We’ve suffered a significant setback with all the damage the Commander has done to herself with this - episode,” she told her team, stubbornly ignoring the slight waiver in her voice and how badly her hands wanted to shake. “Keep her sedated at all times from now on. I do not want a repeat of this, am I clear?”
As she left the operating room, Jacob caught up to her. “What the hell was that?” He demanded, gesturing wildly at the room they’d just left. She shook her head in silent answer. She has no more idea than he does.
“But, Miranda.” He grabbed her by the elbow, dragging her to a standstill, much to her annoyance. “I didn’t even know Shepard was a biotic, and that certainly wasn’t normal biotics.”
She took a deep, focusing breath before replying. “She wasn't before. Her body landed in the eezo field from the Normandy’s Tantalus core. She absorbed so much Element Zero that removing it all wasn’t just a matter of time or cost: it had bonded with almost every single cell of her body. The ones that were left, anyway. We adapted our plans, added the proper implants needed for her to be able to control what we theorized would be exceedingly strong biotic abilities.”
“Yeah, strong is one word for it. She erased Henries, Miranda. That - that’s not normal!” He shook his head in disbelief, and Miranda had to agree with him.
“It doesn’t matter,” she decided, firming her stance and straightening her back, “we need Shepard if we are to have any hope of defeating the Reapers. She’ll learn to control her powers once she wakes up, I’m sure.”
“If you say so, but that didn’t look uncontrolled to me.” She gave him a scathing look, which he interpreted, rightly so, as a demand for him to elaborate. “With the kind of power it takes to entirely atomize a human being, I’ve no doubt that field she was … emitting could have been ramped up enough to kill us all in a second.” He snapped his fingers for emphasis. “She was holding back.”
She dreamt of Shepard that night. Not of how she was that day, but of how the holo’s remember her: a figure of strength and authority, standing proud and strong in N7 armor, though in her dream this version of Shepard had brightly glowing eyes: as if twin red suns had been captured in them.
“You should have left me dead,” she said again, but this time there was no anger in her voice, only a bone deep tiredness; a weariness that was only barely held in check by the unbreakable force of will that Shepard was known for. That the Illusive Man was banking on being the very thing to save the human race.
Miranda opened her mouth, but no matter how hard she tried she could not summon the words she wished to say, and so she was forced to weather the Commander’s withering reproach in silence until she awoke.
This was the second anomaly: every single person working on the Lazarus Project had the exact same dream that night, and every night after, until Wilson’s betrayal. Sometimes Shepard spoke, sometimes not, but always was her reproachful glare aimed their way.
Alarms blared.
Emergency lights flashed.
And Commander Jane Shepard opened her eyes.
Miranda Lawson’s voice came over the loudspeakers, and Shepard was striding towards the locker and pulling on the armor there before Miranda even had a chance to suggest it. Burning red eyes, the same eyes Miranda had seen in her dreams, glared at her through the camera she was watching through. It was uncanny, as if Shepard could actually see her. The feed went static for a moment, and when it cleared Shepard was already out of the room and making her way through the station at a dead sprint.
LOKI mechs were torn apart on the molecular level, shunted into walls with enough force to embed them there as they sparked and died, and perfunctorily shot in short order. She stormed through the station with such speed that it left Miranda gaping, hardly able to keep up on the monitors. She kept issuing suggestions and veiled orders, even as she realized how redundant they all seemed.
The Commander knew exactly where she was going.
“Jacob!” Shepard barked as she came into view of the former Alliance marine, hunkered down behind cover while a small host of LOKI mechs poured out of a door across the way. He looked at her, blinking in surprise, and she motioned for him to stay down.
In the next instant, a Commander Shepard wreathed in a crimson biotic aura shot forward across the chasm separating them from the mechs, slamming into the heart of their formation, before scattering them with a wave of concussive force that shattered their frames and dented the floor, and arcs of red lightning which fried their electronics and scored the walls. The few that remained standing fell to a handful of perfectly placed shots, and then Jacob Taylor watched as Commander Shepard casually floated back across the gap to his side, as if held aloft on wings he could not see.
For a moment he just stared at her, dumbfounded.
“You okay Jacob?” She asked him, concern knitting her brow together.
“Yeah Commander, I’m fine. How-” he started dubiously. “Did Miranda send you?”
“I came for you.” She said, incandescent eyes going distant and voice faint. “I’ll need you and Miranda in the coming months. You and many others if we’re to stop the Reapers and their puppets.”
“You’ll get no arguments from me, but Shepard,” he crossed his arms to hide his nerves, “I need to tell you something.” She just stared into his eyes, her own aglow with a knowing that was frankly unsettling and which had him shifting his weight, unsure of how to say what he needed to say.
“You’re Cerberus.” She said for him when his pause grew too lengthy.
“The uniforms give it away?” He chuckled, but she shook her head.
“No, but there’s no time to explain now.” She turned to look off into the distance, as if looking straight through the layers of walls and blast-doors to the hangar itself. “Miranda’s setting the self destruct as we speak. We have to move.”
“Aye, Commander. I’m with you.”
“Wilson!” Jacob started when they rounded the corner and caught sight of him. “You survived.”
“Only barely,” he gasped out, clutching his leg, “one of the damn mechs got me in the leg before I could-”
Shepard moved, her unyielding hand slamming down on Wilson’s throat and pinning him to the wall he was propped against.
“Shepard!” Jacob gasped, hand going to his sidearm, though he didn’t draw it yet. “What are you doing!?”
“You’re a liar, Wilson.” Shepard growled into the frightened man’s face. “You tried to kill me today when you hacked the station's security and turned the mechs loose.”
Wilson opened his mouth to deny her accusations, but then he looked into her eyes - a pit of hellfire held by a ring of nearly luminescent green - and the truth poured forth instead.
“What do you care? You didn’t want to be brought back to begin with!” Jacob’s eyes widened at the blatant admission. His hand fell away from his sidearm.
“That doesn’t mean that I want to die again!” She snarled. “Not now that I’m back and I can end the cycle once and for all. I won’t leave all my friends to die!”
“Please, the Reapers are just a myth. There is no such thing-” he cut off with a choking noise, fingers scrabbling at her gauntleted hand as she stole away his ability to speak.
“You’re an absolute fool if you really think that after what happened at the Citadel two years ago.”
“How do you know it’s been two years?” Jacob asked her, sure that such a detail wouldn’t have come up, given the circumstances and knowing Miranda as he did. For that matter, how did she know that Wilson had turned the mechs against them?
Shepard ignored him, bearing down harder on Wilson’s throat until his face turned blue, his eyes rolled up in his head, and he finally slumped over. She held on a moment longer, jerking his head in her grip such that his neck snapped, then stepped away from the traitor's body.
“I know a lot of things I shouldn’t. I know that Wilson was bought by the Shadow Broker and tasked with killing me and destroying this station. I know that the Shadow Broker has quite the collection of Reaper artifacts. I know that they speak to him, and he listens.”
“Shit,” Jacob breathed. “If the Shadow Broker’s been indoctrinated, we should-”
“He will die with Liara’s hands around his throat.” Shepard cut him off, glaring balefully into the distance at something only she could see. She said it with such conviction that Jacob didn’t even question it, just nodded his head.
“I believe you.” He said simply. She smiled over her shoulder at him as she started off towards the hangar bay.
“You’re a believer in what you can see and what gets results. That’s why you left the Alliance, isn’t it?” She asked rhetorically, and Jacob startled slightly. “A man of morals and pragmatism who just wanted to actually be doing something, so when Miranda made the offer you accepted.”
He nodded dumbly, not entirely sure what to say. She’s right, and what’s more he knows that Miranda absolutely would not have mentioned any of that. So how-
“Don’t linger on the how’s or why’s right now, Jacob. Later, once we get off this station I’ll answer all your questions as best I can.”
“How did you know what I was thinking?” The words burst out of him, impossible to contain, and her smile fell away, replaced with a firm glare.
“That was an order, Taylor.” She barked, and he was straightening to attention without even realizing it. “Focus on the here and now, we’ll have time for twenty questions later.”
“Yes ma’am!”
Shepard tore through the LOKI mechs with contemptuous ease, pushing forward at a breakneck pace that he genuinely struggled to keep up with. He took it as a challenge, unable to contain his grin as he threw himself at their enemies with everything he had. Out of two dozen mechs, he may have only felled five, but he did so in under a minute all while nearly flying across the station to keep pace with the sometimes literally flying Commander.
She didn’t even seem to realize she was doing it, but as they approached the door to the last shuttle, she wasn’t walking, but floating less than three centimeters off the floor.
The door opened, and there was Miranda Lawson, (im)patiently waiting for them.
“Jacob. Commander Shepard.” She nodded to them both in turn, hand on her hip. “The shuttle’s prepped. Let’s go. My boss wants to speak to you.” This last was directed at Shepard.
The Commander nodded grimly. “Mr. Harper and I have a lot to discuss. Let’s go.” She ignored the looks both Cerberus agents sent her way as she glided around Miranda and made for the shuttle.
“Who’s Harper? And is the Commander floating?”
Jacob just nodded. “Noticed that too, did you?” Then he laughed at the glower she sent his way.
“Before you meet with my boss-”
“The Illusive Man,” Shepard interjected distractedly, thoughts clearly elsewhere, and Miranda blinked before continuing as if Shepard hadn’t spoken.
“-We need to ask you a few questions to evaluate your condition.” They sat across from each other on the last shuttle off of Lazarus Station, Shepard on one side while the two Cerberus agents sat next to each other.
“C’mon Miranda, more tests? Shepard handled those mechs just fine.” He snorted to himself. “Better than fine, you took ‘em down like they were nothing.”
“Husks are more threatening than LOKI mechs.” Shepard scoffed, then turned to Miranda. “Your personnel must’ve been caught entirely off guard to be taken down by that lot.”
“Quite.” She drolled.
“Ask your questions, Miranda.” It was an order, and Miranda tried not to let that bother her. She’d be taking a lot of orders from this woman in the near future. She’d better get used to it.
“We need to make sure your memory and personality are intact-” Shepard cut her off, voice low and intense.
“I watched my family die at the hands of Batarian slavers in the summer of 2170. Joined up with the Alliance the day they rescued me. Had to lie about my age, still surprised I got away with that.” She barked out a short, grim laugh, shaking her head. “I paid the Batarians back for their cruelty tenfold at Torfan. For every man I lost, I cut down ten slaver scum. When they surrendered I had them gathered in their own slave pens, rigged with explosive collars set to detonate randomly over the course of an hour.”
She paused, lost in the memory.
“You should have heard it,” she continued softly, “the shouts and hoots of the freed slaves as they watched their masters beg and cry and die, just as they had all their lives. They call me a butcher, and maybe I am, but I know that that was justice.”
She speared Miranda with a fierce smile. “That about cover personal history?”
“I should say so.” Jacob said, wide eyed. “I always thought you’d just not accepted the batarians' surrender and gunned them down, not that you, uh…” He trailed off, gesturing with his hand as if to encompass all that she’d done that day.
“Strapped explosives to prisoners of war and watched them die one by one?” She finished for him. Jacob just nodded mutely. “Officially, you are entirely right. Unofficially?” Shepard shrugged. “War is dirty, and the brass doesn’t really care what happens to slaver scum so long as the reports are at least somewhat clean. I got our people back and freed nearly ten thousand aliens on top of that. Bought us a lot of goodwill with the Council races. That was all that mattered, in the end.”
“Your personality is definitely intact,” Miranda cut in, glancing at her omni-tool. “Now let’s try something a bit more recent. Tell me about Virmire.”
“Virmire is where everything changed.” Shepard leaned on her knees, steepling her fingers, eyes lost in the not so distant past. “I’d already accepted in my head that the Reapers were real and they were coming, but that mission was where I felt it in my heart for the first time. A sort of dread for which there are no words, knowing that the world as you know it is already over. It just doesn’t know it yet.”
“It was on Virmire that Wrex saw hope for his people for the first time in his long, long life, and it’s where I had to make him see that cloning was nothing but a false hope. It would never save his people from the Genophage. The salarians are the ones that made it, and it will be a salarian that unmakes it.” This last was said quietly, almost to herself, and Jacob wasn’t sure what to make of that assertion. Miranda just arched a single perfect brow in response.
“It was on Virmire that I spoke to Sovereign.” She reached out a hand each, touching the two Cerberus operatives’ knees and - Rudimentary creatures of blood and flesh, I am the Vanguard of your destruction. I am Sovereign - they both jerked back as the voice of Sovereign, like a crushing weight, sounded in their minds. In an instant Miranda had drawn her sidearm and pressed it against Shepard’s temple, but she could not pull the trigger.
Not that she lacked the will to do so: no, she physically could not do it.
Shepard blinked, surprised, then jerked her hands back. “Sorry, I shouldn’t have done that without warning you first.” She frowned to herself.
“What was that?” Miranda demanded, not moving her sidearm, even as the desire to pull the trigger left her like water flowing down a drain. Jacob nodded his head, eager for an answer himself.
“I shared a bit of my memory of Sovereign with you both. I should have known that having a Reaper’s voice suddenly sound off in your head would be somewhat distressing.” An understatement if there ever was one. “You can lower your weapon now, Miss Lawson. I’m not going to hurt you.” There was no lie in her voice or her eyes, but it was the rueful little smile that she shot her way that got Miranda to truly relax and stow her weapon.
Shepard nodded in thanks. “And it was on Virmire that I left a good friend and squadmate to die. Ashley Williams was a good soldier and a goddamn hero, and if there was any alcohol on this shuttle I’d raise a toast in her honor.” She leaned back in her seat, eyes falling closed as she breathed out a sigh. “Any other questions?” She asked without opening her eyes.
The Cerberus agents looked at each other, then turned to her with far more intense expressions than before.
“Yes,” Miranda started, “Just how did you ‘share a memory’ with us?”
“The peak of evolution for all sentient beings lies in unlocking their inherent psionic potential.” She opened her eyes, pinning them both with the intensity of her stare. “In this, too, lies the key to the Reaper’s defeat. Death handed me the key, you played God and brought me back, so I intend to use that key.”
“Psionic potential?” Jacob asked, utterly lost. “Is that like a more advanced form of biotics?” Miranda rolled her eyes at him, to which he crossed his arms. “What? It would explain the crazy things I’ve seen her do.”
“Biotics are to psionics like a steam engine is to modern drive cores,” Shepard explained. “You can’t get to what we have now without first developing the steam engine, and they are used for - nominally - the same purpose: they both power machines of some sort, but the enormous leap in power and possibilities from one to the other is mind bogglingly large.” She looked away, out the window into the vast dark void beyond. “The Reapers have made the leap, and the only thing they fear is another race accomplishing the same. So we will. We’ll unlock our psionic potential and cast these dark machine-gods down once and for all. Bring an end to the cycle of destruction which has held the galaxy for almost a billion years.”
The Commander turned back to them, nothing but surety of purpose in her eyes and her posture. “We are the last cycle. This much I know for certain. The endless chain breaks with us, one way or another.”
Neither of them quite knew what to say to that, even as Shepard’s impromptu little speech had them sitting straighter, filled with the same glorious surety that was within the Commander herself.
After a few moments of silence, it was Jacob who spoke up, unable to curb his curiosity. “So is that how you know so much that you really shouldn’t? Through your … psionic powers?” He asked, somewhat unsure of what to call it.
Shepard sighed, rubbing at her eyes tiredly. “No.” She stopped there, and it was Miranda who pushed for an answer.
“Then what was, Commander?”
“The dead know things the living don’t, Miranda. They know things the living should not. Lazarus may have forgotten all that he saw and learned before Christ brought him back, but I haven’t. I remember everything, and sometimes-” She stopped, looking up at her through the curtain of her bangs, hanging loose and messy around her face.
“Sometimes I get - flashes of insight. Like when I look at you, I see Oriana,” Miranda shot up in her seat, eyes wide with alarm. “And I know that your father will find her if we don’t intervene. It’s only a matter of time.”
Miranda sucked in a breath through her teeth. “I will not let that happen!”
“No, you won’t.” Shepard agreed, eyes glazed as she looked into the middle distance. “We can head to Illium as soon as we finish our business on Omega. Your sister will be fine until then, but Archangel and the Doctor cannot wait.” Her calm assurance was like a balm to Miranda’s riled spirit, and she slowly settled back down into her seat.
“Thank you Shepard. For the warning and for offering to take our mission off course for me.”
Shepard seemed to come back to herself, shaking her head briefly before shooting the operative a genuine smile. “Not a problem, Miranda. I’ve got my own reasons for going to Illium myself, so it’s not even really a detour.”
“What do you see when you look at me?” Jacob asked. “Don’t think I’ve got anything like what Miranda does in the closet to see, though.” He shot the operative in question a teasing look, to which she rolled her eyes.
Shepard looked at him for several long, quiet moments, before finally saying: “Your father will disappoint you.”
“My father’s dead, Shepard.” He said flatly.
The Commander tilted her head consideringly. “Yes, I suppose he is.”
The hologram rose up around the Commander. She stood ramrod straight, arms behind her back, staring straight at the spot where the Illusive Man would be when the connection was finalized.
One second there was just the blank wall of the communications room, the next there he was: crisp suit and crisper hair, legs crossed lazily, cigar held even more lazily as he regarded her with eyes that glowed like neutron stars.
The moment their eyes locked, Shepard’s every thought sharpened and focused upon him. He became the sole beneficiary of her intent and sight.
“Commander Shepard,” he greeted her, casual as you please, smoke wisping out from between his lips. He flicked his cigar into the ashtray at his side. “It’s good to finally meet you.” He said after a moment, when it was clear the Commander wasn’t going to return his greeting.
“You need to listen to me,” Shepard started, eyes intense and voice deadly serious. It actually gave him pause, and he set his cigar in the ashtray to finish later so that he could give her his full attention.
“You’re being indoctrinated.” She declared with the utmost certainty, and he narrowed his eyes at her even as a shiver ran down his spine.
“How-” But she cut him off, slashing her hand through the air as she stepped forward. Energy crackled around her, arcs of red lightning tearing into the space before her and before him, and when she took another step forward the air was torn asunder and there she was.
No longer a hologram, but a towering soldier of unerring strength and will, glaring down at him in his chair as if from on high. She bent down, taking his head between her hands, and the Illusive Man made peace with the fact that he was about to die, but then she did the last thing he expected given her past.
She didn’t break his neck the moment her hands were upon him.
“One of your surgeons, a Dr. Yoriko, was indoctrinated during their time studying fragments of a dead Reaper. They implanted bits of Reaper tech into your head. I don’t think they even realized what they were doing.” There was sadness there, underpinning the strength of her words. Sadness for the surgeon and him alike. “It’s working slowly because there’s so little of it, so it’s not too late.”
“Indoctrination can’t be undone.” He regarded her suspiciously, some part of him rebelling harshly at the idea of him being indoctrinated. “How do you know-”
“It can’t be undone,” she spoke over him, “but it’s not too late for you, Jack Harper.”
He twitched in her grip. “What did you call me?” He asked faintly.
“You need to go to the Citadel. Find Dr. Chloe Michel. Tell her I sent you, have her take all the cybernetics out of you and replace them with stock equivalents. Destroy the ones that were in you. Do you understand?”
A strange buzzing in the back of his mind had him blinking hard, trying to clear it away so he could focus. “That’s a rather drastic thing to do, considering how many augments I have implanted in me. Besides, what proof do you have that I’m being indoctrinated at all?”
“The fact that you’re arguing so hard against doing what I’m suggesting is proof enough, don’t you think?” He opened his mouth to retort, but his words died in his throat as he realized that the Commander was right. That buzzing sensation got worse with the thought, and he winced, wishing he could rub his temples as he normally did when this happened. The Commander’s eyes darted around his face, missing nothing, then slipped closed. Her lips pressed into a firm line as she concentrated, and then that incessant buzzing, which had plagued him for so long he couldn’t remember what it had been like to live without it, was swept away.
His thoughts were unburdened; free and clear for the first time in far too long. He sucked in a breath, and her eyes sprung open.
“I expect it to be done the next time we speak. If not…” The threat was clear in her voice, and he found it oddly reassuring. He knew, deep in his heart where instinct met something ephemeral and unnameable, that what she had done to free him of the Reaper’s influence would not last. He had to act fast. Knowing that, if he failed, she wouldn’t let him become their puppet was a tremendous relief.
So he nodded his head and said: “It’ll be done, Commander.”
She released him and stepped away with a nod of her own. “Good. In the meantime, I’ll take the new Normandy and her crew and go investigate Freedom’s Progress.” Somehow, it didn’t surprise him that she knew exactly what he had called her here to tell her.
“The Collectors won’t know what hit them.” He smirked even as he pulled up his personal pda to schedule both his shuttle to the Citadel and the discrete interrogation of Dr. Yoriko. Who knows how many other agents she’d compromised!
Shepard returned his smirk with a vicious one of her own. “Damn right they won’t.” Energy arced around the Commander once again, and when she stepped back, into the wrent in the air she had made, she was gone. Returned to the station where Miranda and the Normandy awaited her.