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.
Unexpected
The next morning
John sat in the shuttle bay going through the armor and weapon mods he had chosen. The mere thought of going back to that base scared him but it also drove him forward. The feelings where conflicting making him doubt himself one moment and giving him a trill the next.
Charles had modded the Black Widow that had been there just as John said it would be. They had at least another hour to go before the mission would even start. But the nerves kept John from doing anything else. Suddenly the music started. The familiar tickling sensation and the whispers where there.
"Shoot the Machine."
John's hand went up, pointing the gun towards Charles. He fought, against the suggestion.
"Take cover." He commanded in his thoughts back at the Geth.
Suddenly Charles ducked behind a crate. John's hand trembled and the gun dropped to the floor.
The music stopped the second the gun hit the floor.
"Very good Just John, Your response time decreased to 7,2seconds. You are progressing faster then I had predicted. I believe you should have little trouble if the mission involves unforeseen circumstances." The Geth said while it came out of cover.
"Damn Charles shoot you, really? Wasn't that a bit of a hard command, What if i couldn't resist it?"
"I predict a 97% chance you would resist. To tell the truth we have conferred with the newly activated Geth from the Dreadnought." Charles shrugged a bit and returned to preparing the Black Widow.
"So how are the other Geth anyway?"
"The others are doing good considering, but they are eager to study the new data I sent them about Organics."
"So you pocking in my head?"
"We are understanding what it means to be Organic, we are learning with every memory you recover. I start to understand what Legion gave up for us."
John nudged the Geth in the side. "Hey no brooding over him. You showed me what you knew about him. I bet he would be happy if he could see us here."
Kaidan suddenly emerged from the elevator. Wonder was written over the features of the man. "Geez What the hell are you two up to again? Chakwas is getting angry that you're always disabling the security feeds wherever you two are."
"Yes sir major spectre sir." John's grinning stretched from ear to ear while he fake saluted.
"Stop saluting you're doing it wrong anyway. Here I would think that something like that would be muscle memory."
"Nah last I checked i probably was a horrible soldier... What was it oh yeah. Mutiny, stealing a ship, ignoring direct orders. Off course a whole lot of stuff that had enough red tape that the file I got didn't even mention why I was incarcerated for months. Really what the hell did I do that's worse then stealing a ship?"
"You don't want to know half of what you did. Maybe someday you will remember and then I can explain everything. But there are things we can't just tell you." Kaidan looked sad as if he was remembering something that hit a bit to close to home. "Anyway John ready for the mission?"
"Hell Yeah."
30 minutes later the shuttle bay was filled up with their teams all ready in full combat gear.
Liara presented them with the data they had gathered. Mostly estimates of how much resistance they could expect.
John had filled in the bits he remembered about the base. Though it wasn't much most of the time he was being held in his own little room.
Kaidan looked over everyone before addressing John directly. "So who do you want on your team? Charles will cover your technical needs, I will take EDI. So take your pick."
John looked up he didn't really know who to pick. Not that he could remember any of them. "Ehm I have no idea, I'm a biotic and Charles said he has Tech covered..."
Garrus stood up. "Crap Shepard I'll join you, I remember every little quirk you ever had on the battle field and I believe the Major here would profit from taking James as a portable battering ram."
"Hey Scars not cool!"
John laughed when he saw the big marine speak up.
"Shut up Tacco, you know it's true." Garrus' mandibles slightly clicked together.
"I'll get back at you next time we play Scars."
John was concentrating on adjusting the straps from his gloves. "Sure James, next you're going to tell me you tamed a Harvester."
John felt all gazes fell upon him, it made him unconformable.
"Anyway, You're correct Garrus I would prefer James as my personal battering ram. So I want everyone in the shuttles in 5." Kaidan nodded slightly towards John.
John understood, Kaidan had just drawn the attention away from him. The man pulled always through for him, covering his ass whenever he eluded the security. Drawing attention away whenever somebody started making John uncomfortable.
So far the mission was going smooth, John had preferred if there would have been a bit more action.
"John two organics coming in on twelve." The Geth stated while waiting behind a cover.
"Finally, I wondered if Alpha team was going to keep them all to themselves. Garrus wait for my signal." John felt the world falling back together while he commanded his people to take their positions. 'His' people, finally he understood. This had been his people, the ones he could trust blind on the battlefield. Garrus hadn't lied when he said he knew every quirk. The both of them easily fell in a routine as if they had been fighting alongside each other for years, which in a way they had. John reminded himself.
John saw two humans come around the corner, the first one was a young girl held at gunpoint by a familiar face. "Doctor Demikhov" John gasped for air.
"Let me through or the girl dies." As to show how serious he was he pushed the gun in the girls back.
John wanted to kill the Doctor, images kept popping up from torture, operations. The bastard had been the one to implant the control chip in his head. He hated this man with every cell in his body.
Charles must have picked up on his distress, as on que he heard the soft notes from the music through his headpiece. "John, we need to get the girl away from the man. Vakarian can't get a clean shot." The Geth just told him over his headset.
John raised his hands in the air. "I'm going to drop my gun, please don't harm her. Then you are going to take me instead of the girl."
The man was on edge, the girl was sobbing. "And why should I want you as a hostage?"
John slowly laid down his gun on the floor looking up towards the man he hated. "Because Demikhov, I'm worth more to you then she could ever be." John slowly moved his hands to his helm and pulled it up. "Or would your boss forgive you if you lost Deimos again?" John starred straight in the eyes of his former tormentor, moving slowly closer towards them.
The Doctor nodded and pushed the girl to the ground, holding the gun towards John.
John bowed a little down towards the girl. "Go, run towards the exit. The Turian back there will take care of you."
She shivered in fear, sweeping the tears from her eyes with the back of her hand. John reached a hand towards her and pulled her to her feet. She ran in the direction John had pointed her.
"She is save, now the both of us are going back to Phobos." The man snarled under his breath.
John felt the gun being pressed against the side of his head. He took a deep breath waiting for the signal he was sure would come any second.
The tickle at the base of his skull became stronger, the whispers becoming louder. John closed his eyes and let go only listening to what the whispers wanted.
"NOW." Hundreds of voices yelled in his head.
John dropped to the side, flinging a singularity towards Demikhov at the same moment as he heard the gunshot. Charles let the go of the control he had taken over John. A simple "Sorry about that." Came over the headset.
John looked at the floating yelling doctor, he picked up the gun the doctor had dropped. "Why?" He yelled towards his tormentor.
"Because we could, you're our property Shepard."
John was furious, he threw in a warp for good measure and saw the man smack in to the wall as the biotic effects exploded.
"WHY!?" Johns hand pulled back crackling with the blue biotic energy. He wanted to kill this piece of scum.
"John stop it, we should take him in for questioning." The Geth stood behind him and held his arm in a tight grip.
John kicked the doctor in the side for good measure. "You're right, it's just I want to..."
The man started laughing. "You fools you should have killed me while you had the chance." The Doctor pushed a button on a remote. The base flashed with red lights a countdown started. John pulled the man up by his collar.
"What did you do?"
"You won't save anyone Shepard." Suddenly the doctors head exploded.
"Fuck what was that?" John let the corpse drop.
"Ocular flashbang, Cerberus equipment for operatives. John we have to stop the Stations self destruct. The closest terminal is near the labs in the left corridor."
"Go! Garrus the girl?"
"Here, she says there are others held captive near the labs."
"Okay Garrus wait for the shuttle, I'm going with Charles."
Kaidan was caught in a prolonged fire fight in the hangar of the Styx base. It seemed the hostile forces where trying to keep them busy. But to what extend? He had heard some disappointed shatter from John and Garrus that there wasn't anything to shoot in their corner of the base.
It had seemed a good idea, Kaidan was taking a frontal assault through the main hangar, while John would cover the second exit so no one could escape. But it rubbed Kaidan the wrong way that nobody seemed to bother that John's team was moving through the base freely.
Amidst all the shooting it had become clear what Styx was up to. A hostage situation, the one who was trying to escape must have been important. They had heard some of the communications, Charles had intervened as John had almost lost his cool.
But then everything had gone from bad to worse. Now they where fighting against the clock. More civilians and a self destruct mechanism. But the thing that scared Kaidan the most was that the troops Styx where throwing at them didn't seem to stop or retreat after the alarms where triggered.
"Say Major, why aren't these Pendejos fleeing for their lives?"
"Hell if I know James, Theories anyone?"
"Control chips." EDI said over the comm.
"No shit?"
"The one here has a recent scar at the same position as Shepard's chip is located."
"Ah crap it isn't fair if they're making us shoot innocent people." James hit one opponent unconscious with the back of his shotgun.
"Everyone disable, try to avoid killing them. Charles any chance you could block the signal?"
Suddenly the alarms went silent and the controlled people dropped their guns.
"Charles I hope that was your doing."
"Yes, I have full access to the base." a voice said through speakers. "Alenko Major, we don't have much time."
John stood in a room containing the operating table he remembered all to well. His stomach clenched together, he felt sick just being here.
Charles had hacked his way in the security. Now he was talking through the station wide speakers. His platform was only an empty shell.
"Charles everything okay?" John gleamed over the empty Geth shell.
"Yes John, but we highly suggest getting everyone of the base as soon as possible."
John walked in the side room where he knew there where security feeds. "Can you give me access to the stations surveillance?"
The monitors flicked on showing several holding cells where people where being kept.
"Kaidan everything okay on your side?"
"Yeah John, what did Charles do?"
"I think he uploaded himself in the computer systems. Kaidan there are dozens of people being kept here. We're going to need more shuttles."
"And someplace to keep those that are stuffed with control chips. Until we can remove those."
"But where? From what I'm seeing these assholes have people everywhere."
"Guys might I suggest C-sec holding cells." Garrus interrupted them.
"Hmm Citadel might work, Aria has a tight grip on the people there. We just need someone to ask her who she can't deny..." Kaidan sounded serious. "John take the first shuttle back to the Normandy. We'll clean up here. Let Liara put you through to Aria T'loak."
"Ehm, Kaidan you're forgetting something... I have no idea who that is." John felt a slight panic rise.
"I know John, but she owes you big times."
"Okay, I hope you're right." Before John could leave the room another screen flickered on. Recordings from himself, while he was being kept on the base.
"For your eyes only, John." was written over the images.
John took a data drive and downloaded the material Charles had gathered for him.
He planned on looking through the data when he had a moment alone.