Spoilers: obviously content from the games including the Ending.
For the most part this will follow ME lore, just adding and adapting.
Rated M since i don't want to limit what i can and can't do as the story progresses.
Control
John retreated slowly, the moment Kaidan had issued orders to observe the Deimos moon, the whole ship had seemed to spring to life. Everywhere people where reporting to their stations as if they had all been waiting for the moment to finally go back to work.
John really didn't know what to do so he tried to stay out of everyone's way. He thought it best to retreat to his room, at least there he wouldn't be in the way. Once he had finally got the elevators attention there was only a smaller slightly hunched man standing next to EDI's physical form, John noticed how she lend him an arm.
"So EDI this is your slave I presume?"
"Hey, EDI what have you been telling him about us?" The man said slightly annoyed.
"Jeff, that was a Joke." EDI explained as they left the Elevator on the command deck. John could hear them bickering like an old married couple as they walked away.
John grinned a bit, while he waited for the elevator to reach the upper level. As he entered his room EDI's disembodied voice was heard over the comm line. "The ship is in full stealth mode, all shutters must be kept closed until further notice." At least the view of open space wouldn't disturb him.
John walked towards the bathroom and watched himself in the mirror. His eyes still had a bit of red but the scars where smoother, he wondered why Phobos had lied to him. It was clear that it wasn't a big problem to fix him up again, the doc had told him she had done the same thing before.
John was at a loss what to do with himself, there wasn't much here to keep him busy here. He decided now would be as good a time as any to read through his personal files, maybe something could jug his memory again.
Reading his own file made everything just more confusing, who was he? Was he even the same man as everyone expected him to be? If he can't remember who he was would that make him someone different. The questions kept swirling through his thoughts. Suddenly everything seemed so much easier back when Phobos had just told him what to think. Was the part that made him a human also gone from his memory? John couldn't make head or tails from anything, to many questions no answers at all.
Why was he even here? Because Kaidan wanted him to be here.
Nothing else but the thoughts manifested themselves as he thought about the last days. Kaidan had done everything to get him back here. But John what had he done? Made a fool out of himself, hanging on to a person he could barely remember, for the sole reason that he felt safe near a stranger. Because that one man's eyes gave him a feeling of safety.
John started crying, the only person who hadn't expected anything from him and off course John had to do something inappropriate and cling to the man. Hell he had even begged the man to stay and hold him. Kaidan must think all sorts of things.
A knock on the door called him back to the here and now. "Shepard Commander, we would wish to speak to you."
John was stunned why would a AI come here to talk to him. "Come in."
The Geth cocked it's head slightly. "Shepard Commander, your ocular sensors are leaking."
"You mean I'm crying, yes I'm sorry about that." John snorted underneath the tears." And please stop calling me Shepard Commander, I'm just John. I can't remember who the other one was."
"Very well Just John, we wanted to talk."
"Couldn't you just like EDI do that through the comm system? Why come up here in person?" Now John's curiosity was back, why would an AI come up to talk.
"We wanted to communicate in private, we have disabled the security in this room." The Geth looked up to one corner of the room.
"Ehm won't anyone notice that you turned those off?" John pointed towards the small camera.
"Only EDI, and she agreed to the override. The organics on board are to busy with their surveillance of the proposed Styx base. We predict we have a few hours before anyone notices."
John couldn't hide the surprise on his face. "So Ehm Charles what would you like to talk about?"
"We noticed an increase in your neurological activity since the process of 'remembering' began. Also an increase in certain hormones seems to occur whenever Alenko Major seems in close proximity. We do not understand these reactions."
"Wait Charles... You noticed what? How did you?" John was shocked by the things the Geth where revealing him.
"Ah we see, no one has told you that we have uploaded Geth run-time's to the control chip?" If John didn't know better he could have sworn that the Geth seemed Embarrassed.
"No and what does it mean anyway? Are you controlling me right now?" But John already knew the answer, they weren't he had never felt any pressure, never heard a single whisper since he was onboard of the Normandy.
"No, we suppress the functionality from the chip. We can however use the neurological feedback to analyze human behavior... It is providing an Interesting perspective.
"But you could control me if you wanted?"
John felt a tickle in the back of his head, a chill ran down his spine. A soft whisper spoke to him. "Yes, we can." and then his own lips formed words he heard his own voice say. "even more then that."
John slapped his hand across his mouth, a whisper escaped his lips. "Holly Fuck How did you." He and Charles said in unison. Then he felt the tickle disappear and the Geth was starring at the ground.
"Sorry Just John, we thought it was easier to show then to explain. We can effectively control every part of you through the implants."
"Damn, why didn't anyone tell me?"
"We didn't disclose everything of this information with anyone else. We are not interested in controlling you, but thought it was something you wished to know. As we said we are interested more in the new perspective this offers us.
"Shit this is just sick, anything else I should know?" John was angry, not at the Geth but at those who had done this to him. He wanted to destroy Phobos, he wanted to make him pay.
"We believe we can use the connection to reverse the effect."
"Wait Charles you mean I could use the control chip to control you?"
"Yes, but not limited to us." John could swear the Geth had just looked mischievous.
"So Charles you're proposing we test this together and then fire it back at Styx?"
"Correct Just John. We propose a form of conditioning. If successful we should be able to turn it against them."
"Well what are we waiting for? Let's do this."
"We would need something to find something that you can associate with the need to resist control."
John walked over to his desk, pulling out a small data drive. "Music, really old and somewhat unknown. We pick a song. Whenever we do this I would need to hear it."
The Geth took the data drive and downloaded the music to it's platform. "We found one that seems fitting, We suggest daily training sessions additionally surprise drills."
John smiled and nodded. Finally someone was offering him something to do.
Kaidan hadn't even noticed John had left at first. The whole crew had immediately taken positions, Jeff was taking the ship in a closer orbit. EDI and Liara where working through the collected data they had from the Cerberus base. When things finally calmed down and everyone was working on their own tasks he had gone to search for John. When it became clear that the man wasn't on the crew deck anymore he got a twitch of guilt. He should have talked to him, at least ask him if he wanted to be involved.
When Kaidan wanted to go and check if John was in his room Kaidan bumped in to Karin. "Doctor Chakwas, sorry didn't see you there."
She shook her head. "No my fault I was just going to check up on Shepard. His surveillance seems off, for hours I only see him reading at his desk and his vitals are just to smooth."
"Wait to smooth, here I would have thought you would be happy about that."
"I don't know, if he is reading through so much... I would have expected some kind of emotional reaction by now." She tapped her data pad with the vitals of John on them.
"So what did Charles say?"
"No idea he disappeared shortly after we started preparing for possible combat."
Kaidan wondered what the Geth could be up to, normally he stayed in the AI core and used an uplink to EDI if he wanted to do something. "EDI, where is Charles' platform?"
"Charles is not visible on any sensors."
"What how can his platform disappear?"
"We don't know last recorded visual was entering the elevator."
Kaidan pushed the button calling the elevator, when the doors slid open it was clearly empty. "EDI where did the Geth get off the elevator."
"No data available."
Kaidan stepped inside the elevator together with Karin. Taking the elevator to John's room.
The moment the elevator doors opened Kaidan and Karin looked at each other. The music was extremely loud.
Kaidan knocked on the door but realized no one would hear that over the deafening sound.
"EDI stop the music in Shepards room."
"I can't the music is not coming from any of the ship controlled systems."
"John? Charles? Dr. Chakwas is on her way up, she and Kaidan seem worried."
Neither had heard her when the door was forced open. John was dancing around through the room, Charles looked up to Kaidan when he entered and broke in a laughing fit.
"The hell Charles what's going on here?" The seemingly confused Human said.
The music stopped suddenly and John dropped to the floor.
"Ah damn, I think you overdid it this time. Human bodies aren't indestructible." John said rubbing his legs.
"We are sorry Just John, It is hard to estimate how far we can take your platform."
"What the hell is going on here?" Kaidan seemed a bit angry.
"Nothing important, Charles here was demonstrating how the control chip worked. He was just testing how far the control goes." John said, adding a little mischievous grin toward the Geth platform.
Charles seemed to catch John's rouse and added. "The emotional feedback we got was... Interesting. We have never experienced anything like it. We wanted to explore what this 'fun' was organics seem to experience when dancing." Charles fingers made small twitches on the word Joy.
Karin took a scan of John. "Well only some scratches, but I must ask for you two to be more careful whenever you want to try something like that."
"Yes mom." Charles said, suddenly both the Geth and John burst out in Laughter.
"Well I can see I'm not needed here." Karin shrugged and turned to leave. Before exiting the room however she threw a backwards glance. "Next time please let the camera in peace."
"You're really okay John?" Kaidan looked worried.
"Yes, everything is fine. Charles is helping me understand what they did to me and I know when he does something. Don't worry Kaidan, everything is fine" John grinned like a small child when the music started again softly in the background. "Why don't we tell him?" He heard the geth whisper.
"Okay if you're sure. Anyway John want to join us when we attack the base?" Kaidan stood there arms crossed before him.
John leaped up, holding his hand out to Charles who immediately stopped the music. "Like you could keep me away Kaidan."
Kaidan grinned right there he saw some of the old Commander Shepard come through. "I was thinking you could join us to in the second team. Guide us through if you happen to remember the base layout."
"Just John, we should join you if you want to go down there. We can not predict how the proximity to the base influences the control chip."
Kaidan looked over to the Geth platform. "Okay Charles, I trust you to cover his six."
John rubbed his knuckles. "Where can I get some weapons and armor in this place? Someone removed everything from the armor station here."
Kaidan laughed. "Everything is in the Shuttle bay. I believe Steve took care of your gear. Just pick whichever one you like, you used to have quite the collection."
John ran towards the elevator. "Come on Charles, I believe there still should be a nice spare Black Widow in that stash. I never got the hang of the Sniper rifles so you can use mine."
Charles moved it's shoulder plates slightly upward looking towards Kaidan. "He remembers sometimes."
Kaidan's jaw dropped. Could it be he just had to point John towards the enemy and he would remember, that seemed to easy.