A/N: Italics indicate internal thought.

Bold indicates Shepard Reaper speech

Bold Italics indicate Reaper internal speech

Please comment and review

This is my first attempt at a story, so I am open to constructive criticism. Also If anyone has suggestions for the story feel free to give them.

Tools of Destruction

Location: Cipritine, Palaven

Date: 5th June

Time: 1000 CST

Half a dozen Turians sat around a table, all of them watching the news feed on a large screen.

"The entirety of the Turian Hierarchy is reeling from a devastating attack carried out last night by a single individual. The attack resulted in the complete destruction of the legendary fortress Ramiscus and the deaths of hundreds of Turian soldiers, including Generals Fandros and Sanrius. The galaxy wide cyber-attack that broadcasted the devastation throughout Citadel space has also caused mass panic. But what seems to have the citizens of the galaxy most terrified, is the terrorist's declarations that this attack was just the start. And thus, many are left to wonder when will the 'Reaper' strike next? And can anything stop this monster?"

Primarch Tactus slammed his fist on the table, "how could this have happened?!" he yelled.

"We're not sure sir," one of the other Turians responded, nervously, "from what we can tell, he was able to walk around the fortress completely undetected, planting those explosives."

The Primarch glared at his subordinate, "and do you have any possible explanation for how a single human was able decimate several platoons of the Hierarchy's best soldiers?" He demanded, outraged.

The others fidgeted uncomfortably, until one decided to speak up, "we believe the armour must be the reason for that sir, although we have no idea how Cerberus could have created technology so advanced, but we can-"

"IMBECILE!" Tactus roared, getting to his feet and slamming both hands on the table, "is that what you think our greatest concern is? Even if we were to ignore the massive casualties we suffered, the entire galaxy knows that we failed to stop the single greatest terrorist attack in the Hierarchy's history. This will be a catastrophic blow to our reputation as the defenders of Citadel space. What is worse, is that we have no idea where this terrorist is," he sat back down "let me be very clear, I want this wretched human found. I want an example made of him. And I want it done before he attacks again."

000

Location: The Normandy, Agalius System

Time: 2200

Shepard leaned over the sink in his bathroom. He let water pool in his hands before splashing it over his face.

You were too soft back on Palaven Johnny, John gritted his teeth and lifted his head and stared at the mirror, …..it was not showing his reflection any more.

It was showing the skull painted helmet of Reaper.

John couldn't help but growl slightly, the visual manifestation of the presence within him had changed from a formless shadow, to the form of his armour, soon after he had made it two years ago.

"We destroyed the fortress. We inflicted massive casualties on the Hierarchy. The entire galaxy heard our declaration. Nothing further was required," John hated having conversations with this thing, but he had found that simply ignoring it only seemed to motivate it to be more vocal.

You allowed them to flee….. You should have finished the job and slaughtered all of them…. It is what they deserved,

"I am doing this to save our people from the evil of this civilisation," he shouted, he then looked down regretfully, "….and I promised….. I wasn't going to become like those I fought against…not again,"

You speak as if they deserve mercy…. when they do not…

"if they accept that humanity will no longer be slaves then we won't have any reason to kill them," Shepard responded, although his voice wavered slightly.

I see… Your time with those two back on the Citadel has put this naive idea into your head…. you are free to hold onto such foolish notions for as long as you want… but eventually you will witness the true depravity humanity has suffered under them… and then you will accept that the only acceptable course of action is….. Extermination!

The image of Reaper faded, to reveal Shepard's own reflection. John couldn't help but massage his temples, he desperately wanted to believe that during this conflict the alien's better nature, that he knew existed would become more apparent, but he couldn't deny that he occasionally wondered if he was only deluding himself.

Shepard put on his armour and entered the ship's CIC.

"What is the situation on this planet?" He asked.

"Our target is this," EDI said, as her avatar brought up a hologram of a large structure, "from the files I decrypted this facility appears to be a weapons factory of some kind. Ordinarily this would not arouse suspicion, but the existence of this facility is known only to the highest echelons of the Turian Hierarchy. I have also determined that the Hierarchy has gone to great lengths to keep the location of this factory secret from the others Citadel races,"

"Well that's not suspicious at all," Joker called out sarcastically.

"Finding out the secrets of this facility is a secondary objective, remember that everyone," Shepard clarified, addressing all the personnel in the CIC.

"Your correct," EDI confirmed, "from what I've discovered, this factories workforce consists entirely of human slaves, numbering at over two-thousand."

"And our main mission objective is to rescue them. Once they're clear we'll level this place. What is the infiltration plan EDI?"

"The easiest point of access would seem to be this disposal chute," the AI explained, highlighting it on the hologram, "from there you will make your way to the main control room and connect me to the main computer, I will then deactivate all automated defences, lock down the armouries and download all information on the weapons. You will head to the cells and release the prisoners. The evacuation ships are waiting on our signal."

"Everyone understand the plan?" Shepard asked, "Good, let's bring these people home."

000

Location: Baetetia, Turian Facility

Time: 2230

John peered from behind the rocky outcrop to get a better look at factory in the distance. That place is pretty big, it's holding possibly a few thousand humans, and there's also the storage facilities for the weapons they build, why does the Hierarchy want this place kept a secret?

Shepard activated his stealth cloak and began to move. To crawl up the disposal chute, he first needed to jump into the massive incineration pit built inside a large crevice. Most people would find this disgusting, but most people hadn't seen sites as gruesome as Shepard had.

"According to the intel, the incinerators will not activate for three more hours."

"Thanks EDI," Shepard looked down into the pit. The dark made it difficult to see the bottom, but he could make out the faint outline of it. It was quite a drop, but nothing he couldn't handle. Without giving another thought, Shepard leapt down. He hit the bottom with a crunch and a squelch. He set is sites on the exposed chute and made towards it.

However, he stopped dead as his first step was accompanied by a sickening snap, he looked down to try and find the source of the noise….. and was shocked to see that he had stepped on the arm of a human corpse.

Shepard took a small step back in shock at the site only to back step onto another body. That's when realisation finally hit him, looking around, he saw dozens and dozens of human corpses. Spread all over the ground. Buried under other rubbish. Piled on top of each other. This wasn't a garbage dump.

This was a mass grave.

Truly shocking isn't it Johnny…..but hardly unexpected….. they only see us as something to be used…. and then thrown away.

Shepard shook his head several times, and by sheer force of will focused back on the people he could still save. He began to climb up the inside of the chute. His claws easily digging into the metal. He made sure to keep his moves silent as he slowly ascended.

As he got near the top, he could make out two voices, "Three more used up today, I swear we need to get slaves that can last longer," he heard one Turian say. John reached the top and carefully poked his head above the end of the chute into the disposal room. He saw two Turians pushing a cart, he could make out several more human bodies inside. "What does it matter? Is not like it's hard to get more," the other Turian remarked.

Shepard resisted the urge to jump from his hiding place and rip them both to pieces. One of the Turians made their way to the garbage chute, he didn't have time to cry out as Shepard's hand shot out, dug his claws into his head and killed him. The other Turian's eyes widen in panic, but his cries for help were promptly silenced by an energy bolt between the eyes.

Shepard stepped onto the floor, "I'm in," he said into his comms, before activating his stealth cloak.

Shepard carefully made his way through the facilities corridors. As he came to another door, he pushed himself against the wall. When the door opened, to let a guard through, he slipped through himself. He emerged in a huge cavernous space; various crates were stacked around. His curiosity getting the better of him, he opened several of them. At first glance they weren't filled with anything unexpected, weapons and grenades. However, upon further inspection Shepard saw that these were very different from the standard models used by the Turian military, they looked as if they were designed to deal more damage. Putting that aside he looked upwards to see several walkways traversing the room.

"Following those walkways is the most direct route to the control room, be cautious of the guards," EDI advised him. Shepard quickly and quietly, scaled up a nearby stack of crates and leapt onto the walkway.

On his way to the control room he found himself on a walkway looking down on several massive assembly-lines. Working at the assembly lines, he could count several hundred human slaves. Most looking malnourished and exhausted, he noticed one pause for a second to catch his breath, and was rewarded by one of the guards shocking him with a varren prod. He saw another completely keel over from exhaustion, one of the guards promptly started kicking her, but Shepard's HUD had already informed him that she had expired.

From what he'd seen, John had learned that this place worked in several changing shifts, ensuring that the assembly lines ran 24/7. Shepard's fist tightened, deforming the railing he was currently holding. A large part of him wanted this jumped down there and start shooting, but he had learned that charging in headfirst would only put all those he sought a rescue in danger. However, once these people were safe, there would be nothing to protect the vermin here. He turned away and resumed his trek to the control room.

Reaching his target, Shepard once again waited for a Turian to leave the room, then used the opportunity to sneak in. There were three Turians, all sitting down at terminals, none showing any real signs of attentiveness.

"What the hell is taking the Colonel so long? He does know he's supposed to oversee all operations from here right," one of the Turian's asked, seemingly uncaring.

"You know what he's like at this time. I swear he loses track of time when he's 'disciplining' the workforce," another Turian responded.

The third Turian gave a dry chuckle, "Yeah. You know we probably wouldn't need to replace these damn apes so much, if he didn't make such an example out of every worker who falls slightly behind their quota."

All three began to laugh, unfeelingly. They were promptly silenced by three energy bolts. Deactivating his cloak, Shepard walked over to the nearest terminal, activating his omni-tool.

"EDI get control of the systems we need, and let's find out what the Hierarchy is hiding here."

"Understood," she responded, after waiting for a few minutes, "I have gained control of the necessary system Shepard. Now accessing files….. Interesting."

"Found something EDI?" He asked, "Yes. This is not just a weapons factory. This is a weapons research and development facility. Have a look at this…." She brought up the schematics of some kind of bomb on the main screen.

Shepard only needed to study the design for a few seconds before he realised…."Damn…. The blast yield….. But an explosion from that could decimate a hemisphere," he stated in slight shock.

"Yes, they say it's based off a design used to….. all it mentions is preventing another Krogan rebellion. That is not the only file of concern," she brought up another file, this time of with a video attached to it.

Shepard held his chin as the video played. It showed a dozen humans, seemingly left in the rocky wasteland of this planet. A voice then said, "beginning test three of low yield defoliater bomb," afterwards a small object was dropped in the mist of the humans. It exploded outwards, releasing what could only be described as a massive wave of fire. After the wave dissipated, the fate of its victims was revealed. The corpses were completely charred black, but more horrifyingly, they were stuck in their final moments of agony, like some kind of morbid statuary.

"That was only a low yield version, from what I can tell larger ones can encompass an entire settlement. They make remarks about testing these out on several human colonies under the guise of a slaver attack," even though she was an AI, John thought he could hear the disgust in her electronic voice.

Shepard didn't respond though, he merely stared at the screen, his expression unreadable behind his helmet. "Shepard?" EDI enquired.

"These weapons…. they're world killers."

"Correct. Weapons designed to cause maximum damage to a planet's natural environment….. and illegal under Council law," EDI stated.

John clenched his fists, the metal in his gauntlets creaking, "EDI…. What is the status of these weapons?" he asked.

"Most are still in the testing phase, but they seem to have manufactured enough here for distribution throughout the entire Hierarchy…."

"Delete all data," he said suddenly, EDI seemed to pause for a second before responding, "The Illusive man would advise that copying the data for these weapons is the best course of action, so that it may be used to aid our—"

"Delete every trace of these weapons EDI," Shepard cut her off, he paused for a second, "Keep the specs and manifests of the facility though. It might be 'problematic' for the Hierarchy if the rest of Citadel space learned about this."

"Acknowledged,"

"Then let's get what we really came here for."

000

Shepard had arrived at the massive cell blocks. He was standing on another walkway, looking down at a group of Turians currently emerging from one of the cells.

One of them was the Colonel, Shepard deduced from the symbols on his armour. He was in the process of cleaning human blood off an ornate knife.

"Sir don't you think this is causing problems," one of them responded, "we do need all these workers actually… working,"

"don't trouble yourself there is plenty more where those came from. Anyway, they were begging to be released from this hardship, so I released them. Just another act of mercy that these apes do not deserve," the Turian's tone was almost one of boredom.

Having heard enough, Shepard deactivated his cloak and jumped down. He hit the floor with a loud clang, gaining the attention of the group directly in front of him and also the other Turians guarding the cellblock.

They immediately pointed their weapons at him, but some started trembling, "spirits….. that's him…. that's Reaper," many of the guards started mumbling to each other.

The Colonel himself flinched at his sudden appearance but quickly recomposed himself, "so you are the one who attacked Palaven…. You are Reaper," he stated. The armoured figure only glared at him in response causing the Colonel to sweat slightly.

"It was incredibly stupid for you to reveal yourself, and to come to this place alone, but then again it's not like more can be expected of your species," the Turian said.

"I am all that is needed to deal with vermin like you," Reaper responded before pulling out his guns. He fired forward, killing the three Turians with the Colonel, before quickly spinning to face the opposite direction and killing two more Turians charging at him.

Dozens of Turians immediately started to converged on his position, several on the walkways pointed their guns down at him, others on the upper floors of the cellblock did the same. Reaper didn't show any reaction to all the weapons pointed at him. He looked back at the Colonel, who was quickly backing away from him.

"I would also like to re-examine your statement of me being alone," for a second he deactivated the vocabulator in his helmet so he wouldn't be heard, "Now EDI,"

When he began to speak again, is voice was echoed throughout the facility using its own PDA system, "My fellow humans I know you can hear me. I know what has happened to you. Torn from homes. Torn from families. Your existence reduced to a number, and told you exist only at the whims of others. I won't insult you by saying 'I know what pain you have gone through' in reality it is irrelevant. You all know the truth of this place, that you're just waiting for your time to die and be discarded like garbage."

He paused for a second before continuing. Inside the cells, the prisoners began to rise to their feet. On the assembly lines, the workers stopped what they were doing and looked up.

"That is what my purpose here is. I am here offering you a chance to regain your freedom. So… What I ask is: are your spirits broken completely? Are you content to wait for the release of death? Or are you willing to take the chance I am offering? ARE YOU PREPARED TO RISK YOUR LIVES FOR YOUR FREEDOM?"

The second he finished his speech, all the locks on the cell doors deactivated.

Not even a second later scores of enraged humans emerged, yelling their hearts out, and charged at their tormentors.

The Turians barely had any time to react before they were overrun. Dozens of guards were wrestled to the ground as their former prisoners dove top of them, their guns were quickly wrestled away from their grasps, and then they began to scream in pain as those they had spent years tormenting began to rain down a fury of punches and kicks on them, breaking their bodies.

Some on the upper walkways screamed as they were thrown over the railings, and smashed against the floor. A few lucky Turians were able to gain enough distance from the rioting humans and opened fire with their weapons. They were successful in gunning down a few unfortunate souls, but rather than sow despair among the ranks, it only resulted in a swarm of anger.

Some humans quickly picked up the weapons of fallen Turians and opened fire, gunning down several of them.

The Colonel looked around in panic at the deteriorating situation. He looked down the hallway and his eyes locked with the one responsible for all of this. The terror in his heart swelled as the blazing red eyes glared at him. He turned on his heels and ran. Even then, he could hear the footsteps of Reaper tracking him.

The Colonel ran on to a walkway overlooking one of the assembly lines. Looking down, he could tell the situation was even worse here than the cellblocks.

The Turians present were overwhelmed by the massive number of angered humans. The slaves working on the assembly line had armed themselves with tools and the parts they were previously making.

"Hey hinge head, is this the right part?" One human snarled, as he stood over a downed Turian, a metal pipe raised over his head, "No..No, please…I-" his pleas were cut off as his head was bludgeoned, blue blood, oozing from his fractured skull.

"Time for an inspection, let's open her up!" another yelled as he and a two of his friends began to slice into a guard's stomach, using sharp bits of metal.

"Hey this one is working too slowly. No food for a week!" two humans forced a Turian onto the conveyor belt of the assembly line. The unfortunate Turian could only scream in terror as they pushed a button, activating a press mechanism, reducing him to a bloody smear.

The Colonel's knees were trembling, everywhere he looked he saw the guards being brutally murdered. This is impossible… We crushed any thought of rebellion out of these pitiful apes… How could we have lost control so fast….. He tried to rationalise as he continued running.

He activated his omni-tool, "All units, we must get this riot under control. Secure higher-grade weapons from the armouries," he ordered.

"We are trying sir," a guard responded, he could hear the sound of rioting humans on the other end, "the armouries are all locked, they're not responding. We need to…. No, no, AHHHH!" the line went dead."

He ran into one of the large rooms used to store the weapons. He met up with a group of half a dozen Turians, "Colonel….we have to get out of here….. We can't….. We can't…" one of the soldiers was desperately trying to get the words out between laboured breaths.

The Colonel gripped his head with his shaking hands, any response he would have given was cut off as a mob of enraged humans slowly began to approach them. In response the Turians raised their weapons.

"Stay back… Stay back you damn humans," one them said.

Suddenly a large figure shot forward. He delivered a punch into the chest of one of the Turians, sending him crashing into the wall with a pulverised rib cage. He sent another flying with a kick, used the blade on his forearms to slice through the throat of a third. He pulled out his guns, and the last three had no time to react before they were gunned down.

The Colonel stood in absolute fear as Reaper turned towards him, the humans behind him cheering him on. He fell to his knees, "Please … Mercy,"

Beneath his helmet, Shepard was seething, at the Turian's display.

Well Johnny….. do you think… there is no reason to kill this vermin…. after all… I think he's accepted that humans should no longer be slaves…..

No…the monsters like him in the galaxy…. they deserve to suffer for what they done,

"Can you believe it?" He said addressing the crowd behind them, "A proud, noble, superior Turian…. on his knees begging for his life. I believe we should show him mercy,"

The Colonel's eyes widened in surprise at this, before his expression quickly changed to horror as Reaper lifted him by his head, his claws digging into his skull, "after all, he has shown mercy to many humans here, hasn't he?!"

Realising what he was implying, humans began to give roars of affirmation. The Colonel could only scream as his life was drained away.

000

Shepard, still wearing his armour, stood in one of the massive cargo bays of a Cerberus cruiser. One of three that had come to help evacuate the slaves. Although, the cargo bay had been converted into something more resembling a refugee camp. Many were slumped on the ground wrapped in blankets, eating the basic food provided, while those in the worst condition were lying on cots.

He turned away as Joker spoke to him through his helmet, "Hey chief, got confirmation, that everyone's off the planet. So, what we do with the facility?"

Shepard heads began to throb as images of the mass grave he found flashed in his mind, "commenced bombardment. Level that place,"

"With pleasure," the pilot responded.

A few moments later, after the ships had reposition themselves, they opened fire on the planet. The shots hit the ground with the force of an earthquake. Most of the buildings were completely vaporised. It only took a few seconds to destroy it completely.

"Anyway, boss is on the QEC, better get back to the Normandy," Joker said

Shepard looked down from the raised section he stood on, at the hundreds of humans getting the help they had been denied for so long.

"Hey Joker, can you patch through what I'm saying to the other ships,"

Shepard made his way to the railing, as he did so, some of the humans down below noticed him, this quickly spread and soon he had the attention of every human in the cargo bay.

It's not enough…. Not enough to just destroy…. put something better in its place, he mused.

"First, I would like to say, the purpose of our actions today was to liberate all of you, but you owe us no debt. If you have homes you wish to return to, then we will do all we can to help you return there. If your homes are gone, we will do everything we can to take you somewhere where you can start again," he said calmly.

However, I would like you to consider this. Me and all of my comrade's," he gestured to the dozens of crewmembers, "chose this path because we refused to sit by while countless innocent people suffered the horror of slavery."

"We have saved you today, but do not forget there are still millions of our fellow humans across the galaxy who are still waiting for rescue. And we will rescue them, we will not stop until every human slave is liberated!" his volume increased as his speech continued.

"As I said, if you wish to live peaceful lives then we will do all we can to help you. But if there are those among you who wish to aid us in reaching our goal.

The crowd began getting to their feet, their eyes beginning to shine with admiration.

"Then you are welcome to join our fight!" He yelled, raising his fist in the air. The liberated slaves immediately began cheering.

"Make no mistake, war is coming. In all its glory…. and all its horror. The choice is yours as it is everyone's right to choose?"

The cheering continued unabated.

Looking over the crowd once more, a proud smile spread over Shepard's face, "then come my friends. Our freedom awaits."

000

Shepard walked into the communications room. The door shut behind him, the lights dimmed and QEC activated, scanning him.

A second later a hologram of the Illusive man appeared before him, sitting in his chair.

"Excellent, Shepard. You barely stopped to rest after the success of your first mission before you left to attack the weapons factory. I suppose now we should discuss the success of both," the man said in his usual calculating tone.

"I didn't want to take the chance that they would realise it had been compromised. That's why I struck immediately," Shepard responded.

"You need to remember Shepard, you are the best hope of achieving our goal, we cannot afford to lose you simply because you go off on some reckless mission by yourself."

The Illusive man took a sip of his drink, "nevertheless your attack on fortress Ramiscus was a greater success than we could have hoped for. The destruction of the fortress and the massive casualties they suffered will result in a horrendous blow to their reputation as the defenders of Citadel space. Of course, all the Intel we were able to extract will prove invaluable towards further damaging the Hierarchy," his eyes gained a curious look, "but EDI informed me that you abandoned the original plan and fought the entire army yourself."

"An army being decimated by a ship is not unprecedented. An army being decimated by a single foot soldier… That sends a whole new message."

"Indeed," Shepard was unsure whether he saw the man smile slightly. Even after two years John hadn't made any headway in understanding this enigmatic man. To Shepard it felt like this man was seeing angles that no one else in the galaxy saw, and it made him nervous.

"Have the Palaven cells been established successfully?" he asked.

The Illusive man merely nodded quietly in response.

"In regards to your more recent mission. The Admirals are very pleased with the prospect of an impressive number of new recruits"

"Pleased enough that they will stop demanding to know who I am?" Shepard asked sarcastically, he knew their admiration for the weapons he had provided outweighed their suspicion of his secrecy for the moment, but he knew they still didn't fully trust him, just like they didn't fully trust Illusive man.

"What I want to know, is why you didn't secure the design data for the weapons being researched in that facility."

Shepard immediately tensed up as he remembered seeing what those weapons were capable of, "we don't need to use 'world-killers' to accomplish our goal," he responded, gruffly.

"Using that technology, we could have gained might not have been a necessity, the mere idea that we were in possession of such destructive power could have been enough to dissuade our enemies,"

Shepard narrowed his eyes slightly, maybe he's right….. maybe we wouldn't have had to actually use them….. He quickly shook his head to clear it of such thoughts.

"I told you that if I was going to do this, I was going do it my way," Shepard said with finality.

"Holding onto your ideals may seem admirable, but you need to remember we are at war. As much as we may try to avoid it, these decisions need to be made."

John looked away slightly at that, "I do have a larger plan in mind. We destroyed the research data, but we kept other data. We have proof that Turian hierarchy was making illegal weapons behind the Councils back."

The Illusive man looked at him with an intrigued expression, "I see what you're insinuating, but we should hold off on something like that for the moment. We should see what other information we can gather first."

"Take some time to rest 'Reaper', I will have your next mission in a few days," with that he deactivated communications.

000

Location: Baetetia

Date: 7th June

Time: 1200

Turian General Adanius seethed in rage as he looked over the ruins of the facility.

When the Primarch had called him in to that meeting two days ago, he never expected that they would suffer another devastating attack so soon.

"Sir, can I ask what this place was?" one of his subordinates asked, the General turned to glare at the soldier, who flinched under his gaze, "This was a top-secret Hierarchy laboratory, and that is all you need to know," he snarled.

"Sir, we found the survivor," the General heard, turning his head, he saw two more of his soldiers escorting another Turian towards him.

"What happened here?" he demanded. The other Turian was shaking, as he looked up at the General, who saw a haunted expression in his eyes.

"It…It was him…Reaper," he stuttered, Adanius' eyes widened at that. Behind him, he heard a few of his subordinates start to mumble to themselves.

Him again…. How did he know about this place?... The existence of this place is one of our best kept secrets…only—That's it, we thought that the terrorist's only goal was to destroy the fortress…. But it's worse, who knows what other information he's stolen….. Who knows what else he could do.

He glared back at the traumatised Turian in front of him, "what exactly happened?" he asked dangerously.

The other Turian panted slightly, "I don't know, we had him surrounded…then he started speaking…next thing we knew… every cell door just opened and the slaves …every human slave just started attacking us….. It was a slaughter… I had to get out of there."

"So you fled while your fellow Turians died," Adanius said, in a scathing tone. The Turian didn't have a second to protest before the General pulled out his pistol and shot him through the head.

"That is the fate cowards deserve," he said, coldly, and the last loose end that could expose us terminated.