Author's Note: Well hello again, it has been a while hasn't it? (Sorry about that by the way, unforeseen circumstances and all that.) I'm going to university tomorrow, which may or may not affect upload times. Hopefully it might motivate me to do some more writing. At the moment I've got huge writers block, so my next chapter may be a while in coming. Finally, I hope you enjoy my latest upload, It's a bit darker than my previous work, but I really enjoyed writing it.

John sighed as he tapped away at his terminal; once again, he was bereft of sleep. The recurring dreams he had suffered from for as long as he could remember had returned, though they were growing infrequent. By now, John was used to functioning without much rest, though he mostly had neural implants to thank for that; work in project Vindicare often required sleepless nights, and their superiors wanted them to be prepared. John looked bitterly down at the list Tali and Adams had given him; it never ceased to amaze him how there were so many faults on a ship this advanced. Ah well, you wanted some work to occupy your time, now you have it. He thought as he opened up a new programme; apparently one of the engine's primary discharge capacitors was bleeding energy into a nearby shielding coolant system and would require re-wiring. Before John could walk over to the maintenance duct, Shepard walked through the engineering deck door.

'Ah, John, thought you'd still be up.' she said, taking a few steps towards him.

'Dreams kept me awake, what's your excuse?'

'Prothean visions won't leave me alone.'

'Well, at least you know how I feel now.' John said, chuckling softly as Shepard walked over to the railing overlooking the drive core. She was silent for a long time, just staring into the pulsating blue orb that formed the heart of the Normandy.

'Did you want something?' John asked, joining her by the railing. She shrugged.

'Company I suppose, were you doing anything important?'

'Nothing I can't do later.' There was another silence.

'Garrus told me about what you said to him. Seemed to strike a chord, helped him make his choice.' John grunted.

'Good, I've been there before, gone down that road. Killing in cold blood for revenge is not an experience I'd wish on anybody.' Shepard turned to look at him.

'Then why didn't you say that instead of the whole thing about letting Saleon win?'

'Because he wouldn't believe it. I know I wouldn't were I in his position. I had to say something to steer him down the right path, I didn't want him to make the same mistakes I did.'

'So there is a heart in there.' Shepard said jokingly. John smirked at her.

'Hey, don't go spreading it around, I have a reputation to keep.' Shepard just laughed softly, staring back at the drive core. After another long silence, she spoke again.

'He looks up to you, you know that? Sees you as some great, honourable warrior.'

'Me? I'm a survivor, an assassin maybe, but an honourable warrior?' he shook his head, 'I'm just another killer in a galaxy full of them. You sure he wasn't talking about you? You have the track record: holding the line at Elysium, leading the assault on Aigai and now spearheading the crusade against the reapers.'

'You give yourself far too little credit, most of what I've done, I couldn't have done without your help.'

'I still think his trust is misplaced, people who trust me always end up dead.'

'This is about Samantha, isn't it?' it seemed more like a statement than a question.

'So what if it is? Doesn't change anything.' Shepard sighed.

'You're going to have to let go eventually, it's not healthy.'

'We'll see Jane, we'll see.' Shepard took one last look at the drive core before turning to the exit.

'I'll let you get back to your work, if you ever feel like talking… you know where to find me.' she said as she left the room, leaving John alone with his thoughts.

Why is everyone saying that to me? He walked over to the maintenance duct and entered, crawling his way over to the problem area. Upon close inspection, it transpired that a completely superfluous wire had been installed and given inappropriate shielding, causing the electricity to drain into the coolant system. John had no idea how such a serious problem had gone overlooked for so long; if the wire had sagged a few inches further down it could overload the coolant system, causing a catastrophic shield collapse at a rather unfortunate moment. John sighed to himself as he brought his arm up to the wire. At least it's an easy fix. He thought, engaging the plasma cutter in his cybernetic arm, severing both ends of the unnecessary wire. Holding it in his hands, he silently cursed whoever decided it was necessary to add an extra wire to the discharge matrix without shielding it properly. After replacing the metal panel covering the circuitry he crawled back to the engineering deck, only to find Garrus standing there. This is just ridiculous; can nobody sleep on this damn ship? He thought, walking over to the turian's side.

'You okay?' he asked.

'Yeah, I'm fine. I guess I was just tired earlier. Hadn't slept since I found Saleon's coordinates.' John's eyebrow shot up.

'Shit, really? I'm surprised you could stand up after that.' A smile crept onto Garrus' face.

'I didn't, remember?' John laughed quietly at this.

'Good point. You know Shepard carried you all the way to the med bay?' Garrus gave him a strange look.

'No, I didn't.' He was silent for a moment before asking John a question, 'She's very… unusual. Unlike any woman I've ever met. What do you think of her?'

'Why do you ask?' Garrus' eyes darted to the side for a split second.

'Just curious about my commanding officer is all. Everywhere I've served my superiors were all the same: strict, impersonal, professional. But Shepard is…different. I wanted to know why.' John looked over at the drive core, slightly suspicious of the turian's motive.

'Well…there's not much to know really, most of it's in her file. Assuming it's not classified now she's a spectre. Grew up on Alliance ships, wherever her mother could leave her while on assignments. Never stayed in one place for long, so she didn't really have a place to call home. Don't know much about her father except the fact she almost never saw him; doesn't talk about him much. Then there's her service record: led the assault on a pirate base on the planet Aigai, single-handedly defended a pirate attack on Elysium.'

'I knew that already, I was asking about what you thought of her personally.'

'I see. Her psych report covers that: generous, kind, outgoing. In my honest opinion, you'll never find a more humane person, always finds a way of doing things without harming innocents. Believes strongly in trust, loyalty and honour; she'll go out of her way to make friends with anyone on her crew and feels duty-bound to help them.' Garrus nodded thoughtfully before walking over to the door.

'Thanks Thompson, you've given me a lot to think about.' he said, walking into the cargo bay. What a strange man. John thought. Why's he so interested in Shepard anyway? He returned to his terminal with a heavy sigh. I never even found out why he was awake at this hour.

Garrus decided to hit the showers after his talk with Thompson, then head to the sleeper pods to get some much needed rest; to be perfectly honest he really didn't feel like sleeping, but he had promised Shepard and Chakwas that he would. After stripping off his armour and underclothes Garrus stepped into the cubicle, the automatic shower turning on and swamping him in pleasantly hot water. Garrus could remember just how fondly he regarded the showers after the mission on Noveria. He fervently wished he would never be that cold again.

With the hot water running in great rivulets from his plates, Garrus' thoughts once again drifted to Shepard and how she had helped him find Saleon. Not many superior officers would go to such lengths to help their subordinates. What startled him more, though, was that she seemed to be treating him more like a friend than simply as a crew member. Throughout his life, Garrus had precious few friends. Even then, they were mostly military friends and either died or moved on after he left for C-Sec. If someone had told him just a month ago that a female human superior would treat him like a friend, Garrus would have had them sectioned, yet here he was. He didn't know what to make of it at all. The shower began its drying sequence, and once all of the water had evaporated Garrus stepped out of the cubicle and began getting dressed.

'Thompson, could you come up to the CIC? You'll want to hear this.' Shepard's voice came over the intercom. John glanced over at Tali, who was happily typing away at her terminal.

'I'll just be a minute alright?' he said.

'That's fine; let me know what it's about.'

'I will.' John headed towards the elevator, wondering why Shepard would want him on the CIC. After emerging on the crew deck he immediately headed for the stairs. When the doors at the top opened they revealed Shepard standing on the podium by the galaxy map. She turned to face him before motioning him over to join her.

'He's here Admiral.' Shepard said.

'Ah, good.' came the voice of Admiral Hackett over the ship's speakers, 'I have some information you may be interested in. Someone is killing former Alliance scientists. There have been four deaths in the past month.'

'I don't see why this would be of personal interest to me Admiral.'

'I am told that before they left the Alliance they were stationed on Akuze for a top secret experiment.' John was stunned. Of all the things to come up now, it had to be Akuze. He was so surprised by the news that he didn't answer for a few seconds.

'Thompson?' Hackett asked, sounding concerned.

'I'm still here Admiral, what do you need me to do?'

'There is one scientist left from the team, hiding out in the Newton system of the Kepler Verge. What you do with him is up to you. Good luck, and I hope you find answers to the questions you no doubt want to ask. Hackett out.' the line went dead and John turned to Shepard.

'How long until we're there?' he asked, emotion beginning to cloud his mind.

'Half an hour, we aren't that far away.' She looked to the side for a moment before looking back at him, 'Are you okay with this? I mean, it might just be a coincidence…'

'No, it's not a coincidence. Hackett didn't tell us what they were working on and if he knew, he'd have said something, which means the files are sealed, even to him. Those scientists were doing something illegal on Akuze and I have a pretty good idea what that could be. Whoever's hunting them down obviously knows that as well.' John began walking towards the elevator to suit up, thoughts raging through his mind. Akuze had been one of the most traumatic experiences of his military career, and the idea that somebody was behind it, Alliance personnel no less, sickened him more than he was willing to admit. He proceeded to his locker in a near stupor, oblivious to the world around him. It was only after he had donned his armour that he realised the rest of the ground crew had assembled. John turned to see Garrus standing next to him.

'You seem a bit…distant.' the turian said.

'Got a reason to be.' John said abruptly, trying to end the conversation: he really didn't feel like talking right now. Garrus' mandibles widened slightly, but he left it at that, instead choosing to go and have some banter with their resident krogan. John looked down at the pistol he kept with him at all times; it had belonged to someone who had died on Akuze, a corporal. It was a constant reminder of John's past, and the price of leadership. He holstered the gun on a magnetic rail on his back before walking over to the Mako, where the rest of the team were gathered.

'The building housing the scientist is at the top of a long trail up a mountain. The nearest safe landing zone for the Mako is several kilometres away, so Thompson will drop onto the mountain ahead of us and make sure our path is safe.' almost as soon as she finished, the cargo bay doors opened and Joker's voice came over the radio.

'This is your stop Thompson, good luck out there.' John immediately ran for the opening, hurling himself out into the planet's atmosphere. He became surrounded by the familiar roaring noise caused by the air rushing past his suit. From here, he could just about see the building he was aiming for, so he angled himself towards it. Once within range, he fired the deceleration thrusters, bringing himself to a slow halt on the ground. John looked up and immediately froze: there were three rather startled mercenaries staring back at him. For a long time, neither side moved, but unfortunately for John, one of the mercenaries gathered enough wits to point his gun at him. It was, of course, a rocket launcher. Uttering an inaudible curse, John fired up his stealth generator, hoping to buy himself time. Sure enough, the mercenaries seemed even more shocked after seeing a man disappear into thin air right before them.

One of the mercenaries shouted something and began running back to the building. What he didn't know was that there was an invisible sword waiting to clothesline him. The impact sent him to the ground, blood pouring from a huge cut in his throat. John turned to the other mercenaries, who were thoroughly terrified by this point, and began running at them. One raised his rifle, but it was of no use. John batted it aside before sinking his sword into the man's gut. The third mercenary managed to get a few shots off, but before he could penetrate John's kinetic barriers he grabbed the man's neck in one hand and hurled him off the edge of the precipice. John activated his radio.

'There were a few hostile mercs outside the base, they've been taken care of. Looks like the rest of the trail is clear.'

'Roger that, we should be there in a few minutes.' Shepard replied. John looked back at the corpses, deciding to examine them and find out what he could. As he approached one of the bodies, he noticed that there was a hand sticking out from behind a stack of crates. He walked over to investigate and found the body of a man dressed in very unusual armour. The helmet was integrated into the suit and had an unusually large glass visor, almost the size of the man's face. The armour itself was white with a few yellow and black stripes, and there was a logo emblazoned on the shoulder. A very familiar logo. Upon seeing it, John went very pale, anger seething through his mind. He almost went into the base that very moment but something stopped him before he did. Instead he stood there, anger still raging through his mind, trying to rationalise his thoughts. Those mercs are obviously the ones hunting down the scientists, but they haven't left yet, which must mean he's still alive. We might not have much time. Just as he was about to contact Shepard to tell her to hurry John saw the Mako drive into view. Within seconds the team had disembarked and were walking over to him.

'Who were these guys?' Shepard asked.

'Just some mercs. But we've got bigger problems. The scientist was with Cerberus and I think these mercs were the ones going after him.' Shepard nodded before opening the door to the base.

'Then we'll just have to get to him before they do.'

Tali ducked back behind cover, waiting for her shotgun to cool down. There were seven mercs left in the room; John was taking care of two of them so the other five were their responsibility. Her omni-tool beeped to inform her that her weapon was ready for use, so she got to her feet. Three of the mercs were being suspended by a biotic field while the other two were keeping their heads down, trying to avoid the hail of fire that Wrex was directing their way as he slowly strode towards them. Tali decided to turn her attention on the three enemies being suspended above the ground, noticing that their shields were about to fail. As soon as they did, she unloaded her shotgun into the closest merc, sending him flying limply through the air. The second received a headshot, courtesy of Garrus, and the final enemy was riddled with assault rifle fire from Ash and Shepard. Tali looked over at Wrex to see him pick up a merc with his left hand before head-butting him hard enough to cave in his helmet. The other found himself on the receiving end of a shotgun blast. He staggered backwards, clutching at his stomach before falling on the blood-slick floor.

Thompson walked over to the other door in the room, a grim expression on his face, and waited for the rest of the squad. Without saying a word, he pressed the button and opened the door to reveal two men, one of whom held a gun to the other's head.

'Stay back! I have no grief with you! All I want is this—this—' the man with the gun said, trailing off as he looked at their group. His eyes were wide with shock and his mouth was hanging open, 'Thompson? My god. What—how?' Tali looked over at Thompson to see that he was in a similar state.

'Corporal Toombs? What's going on? How did you live?' Toombs' eyes darted back and forth between the scientist and Thompson.

'I survived Akuze sir, thought I was the only one. Looks like you made it out too.' the Corporal's face contorted in rage, 'I found the men who did it, the ones responsible for all the deaths! This scientist,' Toombs almost seemed to spit the word out, 'is the last of them.' Thompson took a step forwards.

'What happened Corporal, where have you been?'

'Cerberus captured me after the attack, wanted to do research on me. They pumped me full of thresher venom! They tortured me, they broke me!' Toombs was almost screaming at this point, 'I don't know how long I was in there, but someone blew up Cerberus and I escaped. Been hunting these bastards down ever since.'

'This man is crazy! Please, you have to help me, I've done nothing wrong!' the scientist said. Nobody seemed to take notice though.

'Do you still hear them sir?' Toombs asked, 'The men, screaming as they were eaten alive by threshers. The men: Adams, Crenshaw, Johnson, Smith, all being ripped to shreds before my eyes! I still hear them; see them every time I close my eyes! I want to kill the bastards responsible for it all, and there's only one left.' the Corporal's finger hovered over the trigger of his pistol.

'Toombs wait! Don't do it! The Toombs I knew wouldn't kill a person for revenge. You're not a murderer, don't let them make you into one.' Toombs looked at Thompson for a long time, tears in the corners of his eyes.

'You're right. I won't let them change me. After all they've done, I can't let them win.' his arm lowered, dropping his pistol to the floor. The scientist turned to face Thompson, the smug look on his face dissolving after seeing the look directed at him.

'Toombs may not be a murderer, but it's far too late for me.' Thompson said in a terribly quiet voice. Before anyone could react, he brought his own pistol up and shot the scientist between the eyes. Tali jumped back in shock: she had never expected Thompson to do something like that. She took a step forward, preparing to shout at him, but then saw his expression. The boundless sadness and remorse she saw in those eyes took her breath away, and she stood there, unable to say anything as the rest of the crew gathered around him. Suddenly, Shepard spoke up, telling everyone to get out of the room and leave Thompson and Toombs in peace. Without a word, everybody began heading back to the Mako. Tali looked back just before the door closed to see Toombs place a hand on Thompson's shoulder.

Tali honestly didn't know what to think anymore. Not that long ago he convinced Garrus not to shoot Saleon and yet here he is, shooting a helpless scientist. Tali's faith in Thompson was extremely shaken and she was unsure of what to do about it. He must have a reason for killing him, it just doesn't make sense.

She began shaking her head. Keelah Thompson, what have you done? Just then, the door opened, and out walked Thompson and the Corporal. The look in Thompson's eyes was staggering: Tali had seen him in a blind rage and in deep sorrow, but what she saw now was much more terrifying; they were empty. Tali couldn't bear to look in his eyes, but found herself unable to stop. Despite everything that had happened, she wanted to comfort him, tell him everything would be alright, and she could tell she wasn't alone. Shepard walked over to his side, worry written all over her face. She raised an arm, as if to hold him, but stopped as Thompson strode past her without a glance. Not a word was spoken as the team returned to the Mako, and from there, to the Normandy.

John stared into the drive core, losing himself in its gentle blue glow. It was once again the night cycle aboard the Normandy and all was quiet as he meandered through his memories. Pretty much everybody aboard the ship had tried to find out what was wrong, but he had refused to talk about it. Even Wrex had made an appearance, though John suspected that Shepard had made him do it. John didn't like blindsiding his colleagues and friends but he felt like he had no choice: John feared that if he tried to talk to them he would reveal a part of his past best left hidden, or perhaps alienate them by getting angry over it. He knew that after a few days he would be fine, be able to put it behind him, but for now his memories wouldn't leave him alone. John heard the door open behind him. He let out a sigh, Speaking of not leaving me alone.

'John, please tell me what's making you like this.' Shepard, wonderful.

'Killing that guy, that's what. Remember when I said that killing a civilian had a price? Well this is it.' John said, trying to end the conversation quickly.

'Bullshit, this goes deeper than that. What the hell does "it's far too late for me" Mean anyway?' John sighed, knowing that Shepard wouldn't give up. Not this time.

'Trust me when I say this Jane, you're better off not knowing.' this just seemed to make Shepard angrier.

'I don't care! I'm not leaving here until I find out.'

'Please Jane, don't make me do this.' John tried pleading with her as he became more desperate, but he knew it was futile.

'Don't make me order you to tell me John, because you know I will if I have to.' he stared at Shepard for a long time, debating what to do next. He had always told himself that he wouldn't tell her for her own protection, but what harm could it really do? They had never kept secrets from each other, never lied.

'You remember when I left project Vindicare, after Jason died?' Shepard seemed taken aback by this question.

'Yes, I do. It was pretty much the first time you were allowed to contact me after you joined them.'

'Well, the truth is… Jason died a long time before that. Four years before, to be precise.' Shepard gasped a little, but decided to wait for him to continue rather than ask the inevitable questions, 'I didn't contact you because I was a wreck, didn't know what to say. I stayed with Samantha on the Citadel for about a month, trying to pull myself together, when Samantha was killed as well.'

'What? I didn't know that Samantha had died!'

'I know you lost touch with her after graduation, so it's no great surprise you hadn't heard about it. Turns out, the people who killed her were also behind the attack on Mindoir. Found out I had survived, wanted to teach me a lesson.'

'Why did they wait until then?' John shrugged.

'Don't know. Never will. After that I dropped off the grid, spent the next four years hunting them down. I killed civilians, innocent people in the pursuit of my revenge. I was almost consumed by the anger and hate, almost lost my mind.' John looked away for a second, 'I'm not too sure that I didn't.'

'Why didn't you tell me?' Shepard asked. She seemed to trying to decide whether to be angry at him or console him.

'I didn't know what you'd think of me, whether you'd hate me for it. Regardless, that scientist was just one more stain on my already blood-soaked hands.'

'So then, what made you convince Garrus and Toombs to spare their targets?'

'I can't bear the thought of somebody else repeating my mistakes. But that scientist had to die. I know how Cerberus works; they would have gotten him out of trouble and he would have been back to experimenting within weeks. He deserved his death, and I knew that I had to kill him, because adding one more kill to my tally wouldn't matter.' Shepard stood there for a moment, deciding what to do.

'Alright.' she said, turning to leave, 'At least now I know. I'll let you get back to… whatever the hell you were doing.' John spoke up again just as she was about to leave.

'Thanks for that Shepard. I feel…better now that I've got that off my chest.' She turned to face him, flashing him that special smile he'd never seen her give to anyone else.

'Hey, it's what I do.'