Spoilers: obviously content from the games including the Ending.

For the most part this will follow ME lore, just adding and adapting.

Kerberos

John was guiding Charles towards what remained of the Crucible docking station on the Citadel. His feet knowing the way more then he himself could remember.

"We won't have much time until a certain someone will discover we disappeared." The Geht walked slowly behind John.

"I know, but until I know this works I really don't want to have to explain this insane plan. Hell Kaidan would probably try to keep me from doing this." John could see the old memories resurface when he looked at the long dirty corridor.

"About that, I can't understand why one such as yourself would pursue a relationship with another male. You would never be able to create offspring, your positive traits would die out."

John let out a soft chuckle. "Charles it's not about just creating new life. Kaidan just makes me feel complete. Besides since when do AI's concern themselves about such things?" John remembered this hallway soon they would reach the large empty hall where everything had started, or ended depending how one looked upon the events.

"I have gathered massive amounts of data ever since I joined the Normandy. We now understand more about organic life, more then we ever could have imagined in the past. You are so complex, so unlike our consensus. The more we learn about those emotions and thoughts organics have the more we see how the old machines were wrong."

"So while you are in my implants you're studying us?" John knew it would only be a few steps until he reached the point where he supposedly died."

"Yes."

John stopped turning around to face Charles. "Maybe it's a good thing, I don't say I like the thought of this, but maybe if those reapers would have taken the time to learn how we think... Well maybe they would have understood us."

Charles cocked his head to the side. "No, they couldn't have. They had no interest in understanding Organics. Their reasoning was flawed."

"So why are the Geth and EDI different from them?"

"We evolved to become sentient, we are still evolving. The Reapers just followed a badly implemented program. We learn and adapt, just like Organics do. We understand that the strength of life is not being perfect but in striving towards a better future, that the road toward that future is what makes life possible in the first place. In the end the only way for both organics and synthetics will lead towards the same goal."

"Then what is our goal, because I have a hard time seeing it with all the bad things in this galaxy." John's gaze followed the path that had led him here, seeing shadows of a past he didn't want to remember right now.

"To create a future where we can understand each other. A future where the mistakes of the past wont be repeated. But to have a chance at a better future we must first destroy the ghosts of the past, Cerberus has to be the past. The reapers where the past. To achieve a better future we must be willing to fight for it."

"I hope you're right Charles, because I can't stand to think what horrors await us if we finally defeat the Illusive man. What's next? Ancient squids from another galaxy? Outer dimensional spirits? I just wish it would all finally end."

"Don't worry about what's next we should only concentrate on the task before us. One step at a time." Charles took a big step forward as to make a point. John shrugged his shoulders and followed.

John stood still taking in his surroundings, only flashes of what happened remained in his memory but it was enough to feel a deep sadness overcome him. "I was sure this would be the end." He whispered.

"Yet you're still alive." The Geth pushed a large piece of debris to the side, clearing a path towards the console in the middle of the room.

"Yes and no, I know I died somewhere down there in a pile of ruble. But Miranda keeps bringing me back, maybe I should finally stop all this fighting, maybe it's time to stop and just live a normal life for once." John touched a particular dark spot on the ground. Words pushing to surface. "Best seats in the house." John sat on the floor, lost in his thoughts.

"Those humans of your's are actually doing just fine. I just keep them locked up to be sure." Aria pointed towards the big cells in C-sec headquarters. "So when will you take them of my hands? I have a station to run after all."

"Miranda will oversee the removal of their control chips, once that's done we will gladly sent them back to their families." Kaidan had gotten used to the big ego of Aria. She wasn't even that hard to understand, she looked out for herself first and her people second. For the moment that included everyone who followed her orders on the Citadel.

"Fine, but please see to it that they are gone as soon as possible."

"We will, we only need to find the headquarters and put a stop to all of this." Kaidan just wasn't sure when that would be.

"Well then see to it that you do just that, now run off like a nice boy and do your fucking job." Aria waved her hand dismissing Kaidan before she moved towards Bailey who appeared in the door. Oh and Major, inform Shepard that his apartment was largely undamaged. He might want to restock the bar though."

Kaidan nodded before returning towards the Normandy, at least now he knew where to hold their meeting with Admiral Hackett.

"Charles the Geth you requested are docking with the station. I sure hope you know what you're dong. I had to pull in a few favors with the admirals for this." Tali's voice haled through the room.

"We appreciate this creator Tali'zora. We wouldn't have asked if we weren't sure this is the right thing to do." Charles blanked out on the spot.

"Not that they could stop you anyway, they just aren't too keen on letting the few functioning platforms wander off at the moment."

"I'll try not to break them too much, Tali." John joked over the comm line.

"Keel'ah, Just don't destroy them, we're having a hard enough time as it is restoring the platforms and they are the only ones willing to work the reaper salvage yard."

"Don't worry Tali, just get their connection to EDI's AI core working." John started disassembling his guns putting the parts out in front of him.

"The other platforms will be here shortly, we should prepare."

John only nodded slightly, loosening the straps of his armor. Laying the pieces next to his disassembled weapons. Once he sat stripped down to his under armor he pulled a small device and set it up in front of him.
"So You might want to strap my hands behind my back, just in case. Biotics don't work too well when I can't move.

Charles, didn't move. John guessed he was interfacing with the console he had been working on. For a long while there was nothing John could do but wait until everything was in place. His thoughts wandered of towards Kaidan. He had felt bad not telling him what he was planning to do here.

But he just couldn't tell him, Kaidan would have tried to stop him or worse insist on helping. John couldn't have gone through with this if it might endanger Kaidan. No it is better this way, still he felt miserable.

"Charles if this goes wrong... Could you tell Kaidan I'm sorry?"

"No, we won't. We will see to it that there is no reason to be sorry." John was startled as a Geth spoke behind him.

"Damn you guys are sneaky, Here I thought giant machines would make more noise."

"We upgraded our platforms." The Geth walked over to the pile of Johns arms and armor. Placing everything in a large bag he had brought. Two other Geth Loaded up their weapons with tranquilizers.

"So how many of you are actually here?"

"Over 12.000 runtimes, not Including the ones you call Charles." The speaking Geth, took out several ropes.

"Ehm I thought you would just tie up my hands or something?" John was looking over to Charles who still hadn't moved. "And why is Charles still not moving?"

"Charles is integrating us with your ship's AI. He will join us as soon as we are ready to begin." The Geth held out the rope waiting for John's okay. "We analyzed the data we had on you, we won't take any risks."

John hesitated for a moment, everything felt surreal. Then stretched out his hands towards the Geth kneeling before him. "I assume Charles explained the details of this?"

The geth tested his own knots before stepping a few feet away and examining the small device John had placed earlier on the floor.

"Say, you guys have names?" John tried to find a somewhat comfortable position.

"Negative"

"Okay then Negative, just warn me when we are ready to begin.

"Negative was an answer not our designation."

"Organics require names to keep living beings apart, they also seem to have a habit of giving names to their favorite guns and toys." Charles turned around. "Everything is ready John, if you want we can start."

"No time like the present, I guess. Negative would you care to do the honors and turn on that music." John kept his eyes focussed on an imaginary point somewhere above him. Only feeling how a large metal hand pressed a small device on the base of his skull.

In the distance he heard the music start, immediately he felt the device buzzing in a soft vibration.

Kaidan had searched the whole Normandy, nowhere John was to be found. "Edi where is John?"

"John is in his room."

"EDI stop lying I just left his room, he wasn't there. You sent me towards the mess hall and he wasn't there either. He wasn't anywhere you said he was, so what the hell is going on here?"

"I..." The lights aboard the ship turned off. After a few seconds the emergency lights switched on.

"EDI? What the hell happened?" Kaidan ran towards the elevator. "EDI? Shit and off course the elevators are out of business too."

"Kaidan, we are experiencing some problems with the AI core. Something is overloading our systems, it's like someone is draining all the power." Joker sounded worried.

"Joker anything from EDI?"

"She just blacked out, it's as if she isn't here anymore."

Kaidan turned around making his way towards the AI core. "Okay Joker start the evacuation protocols, I want all non essential personnel off the ship. I want Tali and Adams in the AI core to meet me there ASAP." Kaidan felt uncomfortable first John had disappeared and now the whole ship was running havoc. Something was going on.

Kaidan oped the door to the med bay, with in an instant he recognized Doctor Chackwas through a dense smoke. "Put some medi-gel on those burns and then move him to the mess hall. I want the Med-bay evacuated immediately." She said in an astonishing calm tone towards two of the crew." Kaidan thought he had landed right in a battlefield a thick smoke had filled the room, half of the equipment was thrown over.

"Chackwas what's going on here?"

"Nothing of importance major, just a small technical problem." She ran towards a man lying on the floor. "Major you should leave, the air isn't the best here at the moment."

"Karin what the hell is going on here? The ship lost all primary systems and then I find this..." Kaidan waved with his hand. Then he noticed the man next to her was Engineer Adams.

"Damn Alenko, the AI core just has some minor problems, Tali is fixing it. We should leave here immediately, now either go or help me carry him out of here."

He heard the voices in the back of his head, a mixture of words softly communicating ideas. The words felt good making him feel safe once again, nothing bad could ever happen if he gave himself up to them. They promised a bright future a better universe, one where they wouldn't be looked down upon. A universe they could shape and lead, making it better than it had ever been before.

No one would ever again have to suffer, no one would ever again lose their loved ones to the intruders. They only needed to work together to shape this future. Once they take over the governments of the universe they won't ever have to fear the future anymore.

The words where compelling, John didn't want to lose his friends again he didn't want to die again. It would be easy just give up the last bit of control and they would never have to fear anything again. If he could just free himself and join the others, his body struggled but he was restrained. He couldn't move, couldn't reach for a gun and join the other whispers in their fight.

Something was disturbing the words, trying to cover them up. A few notes played in rapid succession before an angelic voice broke through. The singing was more present, more real than the whispers. He concentrated on the voice. It was as if it was speaking directly towards him.

The one singing asked a question, a question he couldn't answer.

"He can't take anymore we have to abort."

"Negative, this is our only chance. We are almost done, change the direction of the Jupiter satellites."

"We have to help him. The signal is getting to strong, he will turn any moment."

The question bothered him, on the one hand he wanted to say he wasn't sure. On the other hand the whispered where promising he would be able to get it.

But there was something else the singing voice offered a promises of its own, and a warning. The warning that no one would wait forever.

The whispers suddenly stopped, only a single voice cut through to him.
"Join us Deimos, be our hero. Be the one to lead Humanity for us. Become the most powerful man along my side."

He thought about it but the singing voice had offered something greater than power, something more important.

"NO!" He yelled as his body fought the restraints. His Biotics engulfed him in a blue wave of energy, ripping apart the ropes that held him down.

Immediately three Geth pointed their guns towards him. Every instinct told him he had to run, but there was a fourth Geth calmly kneeling beside him, removing a small device from his neck.

"John, we have their locations... It's worse than we anticipated."

The systems on the Normandy came back on-line suddenly. Kaidan ran immediately back towards the AI core. "Tali what the fuck is going on?"

"Nothing we can't handle, the Main processors just got a bit overheated. The system wasn't really designed for so much data to be processed at once. When the cooling failed we had a minor heat problem. Nothing we can't fix."

"What data? Why isn't anyone telling me what is going on here..."

"We have our orders, don't worry about it EDI should be back online the moment I can find out what cables need to be replaced.

"Damn Tali next time warn us that something like this might happen. And can someone now tell me where the fuck John is?"

"He's away with the Geth, but before I say anything else you should just talk to him yourself."

Kaidan wasn't sure what to think anymore, not only was John up to something, but he had seem to think he couldn't tell Kaidan what it was. " This is getting annoying Tali, where is he?"

"Crucible docking point, where Anderson was found."

Kaidan stormed off, he didn't know if he should be worried or angry.

John calmed he remembered the Geth's voice. The one that sounded a bit more passionate than the others. "I.. it was..."

"I know, I'm blocking them out. I'm sorry but we had to make sure we located all their bases." Charles offered him a hand pulling him back to his feet.

"So where is their main base?" John swept the sweat from his forehead, the whole ordeal had taken more out of him then he had ever imagined.

"Styx and Kerberos"

"I know Styx is Cerberus so where are they?"

"No their main bases are located at Styx and Kerberos."

"Wait they even stole the names of the base for their organization?" John felt incredible dumb, why hadn't they just checked the extranet.

"John you are looking a bit pale." Charles reached him a bottle of water.

"Just a headache. So do we have enough to find them all?"

"We think so, we where able to upload a few Geth in their mainframe. They send us as much as they could find without being discovered. The Normandy had some problems due to our up-link but Creator Tali assured us she can handle it."

"Wait those Geth are still in their database?" John tried standing up, the world spun around him and he had to sit back down.

"Yes, they will remain and try to update us if something changes. It was decided that they should stay behind to sabotage the system when we attack. Now we should return to the ship, before someone gets worried."

AN: Sorry it took so long to update, life somehow got in the way.
Anyway on a side note when I started writing this I intended to use two unnamed objects near the dwarf planets for Cerberus and Styx base and just name them accordingly... Someone did me a favor a few weeks ago, Kerberos and Styx actually became officially the names of the two remaining Pluto moons. But I'm still sad Pluto isn't a planet anymore no mater if the moons now are all Greek mythology related to the underworld.