Spoilers: obviously content from the games including the Ending.
For the most part this will follow ME lore, just adding and adapting.
Rio
John closed the visor of his helmet. Taking a moment to gather himself before he opened the shuttle door.
"Steve get back in the air and cover us. See if you can get through to Kaidan."
"Yes Sir."
John jumped of the shuttle standing in the middle of the airstrip. "Shit not much cover here, let's hope we don't have to fight our way through the complete base. People chances are if Styx has their hands in this we need to fight through hordes of our own. Try to stun and disarm."
They ran a few paces away before the shuttle took of the ground.
"Say I don't know how it's done in your Alliance base, but if an alien and a giant machine jumped of in full combat gear in the middle of a Turian base... Well let's say why doesn't anyone stop us?"
"Yeah, specially since there are turrets on those guard towers, and normally they would be alarmed by an unauthorized shuttle taking off." John stopped for a moment looking around. "Shit this is wrong, not even a person in the open? This smells like a trap." John turned around finding his way towards the shooting range.
"What now?" Garrus sounded slightly nervous.
"We go through the maintenance tunnels under the base. I don't feel like walking in a trap on an open field."
Kaidan's head was throbbing, as he woke up he had a hell of a migraine. Grateful that there wasn't any bright light that would make things worse.
But where the hell was he? He recounted the events, they had come to the base in Rio some General had been eager to talk to him while James checked in for N7 training. Shit James, where was he? And EDI last he saw her she had wandered off to find a terminal. He had to find them. Kaidan struggled to get to his feet, he felt dizzy.
"Major I should have guessed you would manage to get yourself caught. Please tell me that Shepard is on the way." A female voice sounded through the dark.
"Who wait, Miranda? Shit where am I?" Kaidan found a force field on one side of the room baring his way out.
"The brig, they keep those they imprison here before implanting them." Her voice sounded with regret.
"So you send the message to John? And why are you here anyway?" Kaidan's eyes slowly adapted to the darkness surrounding him.
"I was caught by Cerberus or Styx as they now call themselves shortly after the war. They used me to implant those soldiers with control chips, when I overheard that they lost Shepard I tried to contact him. Hoping he would have broken free of them."
"Geez Miranda why didn't you just contact me or EDI? John isn't really himself at the moment. He has only escaped the control chip due to a Geth upload in his implants. and why aren't you under their control?"
"They needed me to bring him back to life, his implants failed some of those where reaper tech. Cerberus couldn't risk loosing my expertise, so they rather forced me to work for them. Major, I fear they will force me to implant you next."
"They won't, John can't be far. He'll find a way to reach us in time, he has to." Kaidan hoped he was right.
"Another explosive at this Junction, this should run directly under the South-eastern guard tower." John pointed at the spot he had in mind.
"Not that I mind-blowing things up but why are we doing this?" Garrus set the explosives.
"Should we have to fight our way out, well let's say I remember that tower sinking of slightly because the tunnels here are a bit unstable." John watched down the tunnel. "Okay still clear, next junction we should be right under the medical facility."
John felt uneasy they had been too long in these tunnels and still no one had tried to stop them. It was as if Styx wanted them to walk right in.
"John we have lost contact to Normandy, it seems something is blocking our communications." Charles walked back towards the last junction. "There is a disruption signal, we lose our ability to communicate if we go further down that tunnel.
John thought about the situation at hand. "Set a beacon if we aren't back in communications rang within 30 minutes send out a distress call to the Normandy." John set the alarm in his omnitool. "Let's move forward we haven't got far to go."
They hurried along the tunnel, turning around the corner at the last junction. John's heart was racing, what if he was too late? What if he had lost Kaidan? He didn't want to think about those things, but the questions kept bothering him, making it hard to concentrate. He hurried up the ladder hopefully leading him towards Kaidan.
"So this is their main base?" Kaidan had adapted to the darkness, now he could recognize Miranda clearly in a cell across his.
"No, geez how stupid are you people? The Rio base is where Cerberus started recruiting from among the Alliance. Really didn't any of you pay any attention? They spent years using your own people recruiting them from the training facilities."
"Okay but where is their headquarters?" Kaidan wondered how long Miranda had been kept here, he could clearly recognize her hair hanging loosely in unkempt strains.
"I don't know for sure but from what I could overhear they are in an old abandoned facility. Going by the amount of time it takes a shuttle to reach them and return I would say pretty far out near the edge of the Solar System."
"Wait you're saying they are right next to the relay?" Kaidan
"It would seem the most logical thing for them to do. "
A door on the far end of the hallway opened and flooded the corridor with light, Kaidan flinched away form the bright light that immediately made his headache worse. "Miss Lawson that's enough or should we torture your sister?"
"You wouldn't dare. You know your boss still needs my coöperation!" Miranda kicked against the wall in anger.
"Well that's right miss Lawson and right now the boss wants you to make that one obedient." The heavily armed guard walked in as he pointed toward Kaidan.
Kaidan was about to protest as the guard pushed on a control panel and gas started pouring in his small cell. "Sleep tight idiot." The guard smirked as Kaidan fell unconscious.
John watched around the corner, quietly signaling the others to take cover in the hallway. "Two armed guards in front of the doctor's office and another two in front of the infirmary."
"If they sound the alarms we won't have much time before more will show up." Garrus exchanged the ammunition mod on his riffle.
"Yeah, I might have an idea." John holstered his gun and walked down the hall.
"Shit, he isn't really..."
"There is a 85% likely hood they will see through his bluff." Charles stowed away his sniper rifle and pulled out the small pistol with a silencer. "Then again organics never seize to amaze me."
"In their stupidity or in their dumb luck?" Garrus followed the Geth's lead.
"Both... Normandy's enemies seem to be more stupid than the average."
John walked up towards the Infirmary's doors before the two guards raised their guns. "Halt no one gets in without the bosses permission."
"Yeah about that, I really need to see the prisoner, He has crucial information on some rogue elements who infiltrated the base." John hoped he was right in his assessment they had one of his people locked up here.
"We need to check that with the boss."
John's Biotics flared up trapping both guards in a well placed singularity. Behind him he heard to soft popping sounds and the other two guards dropped to the ground. A few seconds later the guards in front of him where dozing off both having a small arrow in their necks.
"Let's hope these tranquilizers Chackwas cooked up hold them down for a while." Garrus stepped over one of the guards searching through his pockets.
"We should put them somewhere they won't be found." Charles dragged two men at once back behind the corner.
John nodded. "Throw their weapons down the maintenance shaft."
"What's taking you so long? The boss said to implant him." The marine got impatient.
"Damn man he's an L2, I can't just pop his skull open and throw in an extra implant. He isn't some stupid grunt like the rest of you, if I'm not care full his implants could overheat or worse his Biotics get uncontrollable and you would want to be torn to shreds just because he sneezes would you?" Miranda was stalling, yes. But if she couldn't prevent this from happening she would at least try to sabotage the control chip as best she could.
"Well hurry up, you need to do finish the other one up before his friends notice him missing."
Miranda took a deep breath studying the scans one last time. "If you think it's so easy why don't you study medicine for a few years and become something more than a mere meat pile. Anyway the moron who did his implants back in the day was a brute, if I could just replace his implants with something adequate, you don't happen to have any L5 implants around here?"
"No, now do your work or should I start my career as doctor by rearranging your face?"
"I get it, just give me some space to breath. I need to design a new wiring for this to work."
"Just get it done." The marine walked back towards the door holding Miranda at gunpoint.
At least now she could try to redesign the chip so Major Alenko might have a chance of resisting the control chip.
John slipped through the doors of the infirmary, two marines where standing with their back to him. Another one was sitting at a desk at the end of the room. On a gurney James was strapped down and looked as if he was sleeping.
John held his gun behind his back and cleared his throat. "Sir, I've been told to pick up the prisoner."
"Yes? Funny I didn't issue the order." The man pushed his chair back and the two marines spun around to face John.
"Yeah, well maybe since the order came from me." John sprinted forward throwing a shockwave towards the two marines before dodging behind a medical cart.
"Really I could swear he's even more reckless than he used to be." Garrus remarked while kicking the door open.
"Probably, is this what you organics call an emotional response." Charles Shot at one of the marines who was struggling to get back on his feet.
"John emotional? He was the most level-headed human I ever saw." Garrus took cover behind one of the hospital beds.
"Maybe then this is the human reaction stemming from a threatened lover?" Charles walked through the middle of the room. When a bullet hit his shields he cocked his head. "I calculated you will have to exchange your thermal clip before my shields go down. I must insist you surrender."
"Wait John and lover? Are we talking about the same man?" Garrus leaned out the side and shot a tranquil arrow in the leg of the second marine.
"Shut it both of you." John leaped over the cart shooting towards the officer. "Ah these little arrows are crap." John grabbed his other gun.
"That's just because you're aim is horrible." Garrus looked up seeing the Officer taking a shot at Charles and decided to overload the mans shields.
"Thanks couldn't you have done that 15 seconds ago?" John's Biotics flared up and he pulled the man towards him. The officer landed directly before Charles feet who knocked the man's gun away across the room. John lowered his gun, walking towards the struggling officer.
Charles cocked his head slightly to the side while he lifted the man up by his shoulders. "No implant detectable."
"What the hell you freak let me loose."
John opened his helm up seeing the instant recognition in the mans eyes. "Nope he's the worst kind of ass hole... One who joined Cerberus of his own idiotic reasons."
"What should we do with him?" The Geth turned his head to face John.
"First mister moron here will tell us where Kaidan and EDI are. Then he will be so nice and disable the scrambling signal that's blocking our communications and maybe then I won't have to ask Garrus to give the poor fool a first hand demonstration of how the Turian special forces extract information." John blinked towards Garrus.
"Oh but those demonstrations are my specialty... They speak of those on Omega even Years after I left that place." Garrus rubbed his hands.
Charles looked as if he didn't understand anything anymore. Before he could speak however the man broke together in a sobbing voice. Spilling everything he knew.
John was already planning their next move. "Garrus tie up those two marines and see if you can wake up James somehow. Charles make a nice package out of this scum bag. I want to make sure he can't get away."
John searched for anything they could use as makeshift restraints. "Oh and one more thing..." John drew his gun and shot the man in both legs.
The man howled in pain, before Charles knocked him out.
"I can't understand he was already constrained why did you shoot him?" The Geth looked puzzled.
"First he can't run off now, second he liked to 'play' his prisoners." John reloaded his weapons. "If we are done here we need to get to Kaidan before they can put a chip in him.
Miranda couldn't stall anymore, her guard was getting agitated. Sadly she hadn't heard any fighting or even a single communication that could give her a reason to think Shepard was really on the way. "I'm sorry Major." She whispered as she picked up the scalpel.
She made the first incision exactly along the old scar from his implants. Silently scolding at the brute who must have done the L2 implant, she tried to remove as much of the scared tissue surrounding it as she dared. Constantly watching on over the scans monitoring every move she made.
A knock at the door made her jump up as she lost her concentration. "I can't use any distractions, could you please do your job for once and see to it that I'm not disturbed." She snapped at her guard.
The doors flew open, a tied up man on a bureau chair rolled in the operation room, Losing balance as the chair rolled in and toppled over. The guard drew his gun and walked towards the swinging double doors. Before reaching the doors Miranda threw the scalpel in her hand in the guards neck. The guard stumbled over his own feet falling headfirst through the doors.
"Really now they start committing suicide before I get to shoot at them." The familiar male voice came from outside.
"Yeah, shoot at them is about right. But actually hitting a target that's something else completely."
"Shepard? Garrus? What the hell took you so long." Miranda crossed her arms in front of her.
"Ehm hello, I guess... and you are?" John took a big step over the dead guard. Looking around to access the situation John's eyes fell on the operating table. His head spun, everything turned black and he sank to the ground.
"Great, Charles what's wrong with him?" Garrus kneeled beside John turning him over.
The Geth dragged a half sleeping James along kicking the dead guard aside while he entered the room. "Increase in Brain activity, Rapid eye movement. He is experiencing some form of intense memory."
Miranda applied medi-gel to kaidan's incision and bandaged him up. "So why did it take you so long, Garrus? I couldn't stall operating the major any longer. Thankfully you came at the last possible moment."
"We took a more hidden path inside, strangely we have barely encountered any resistance."
"Get the major off this table and bring Shepard here. I need to see what those fools did to him." Miranda dragged a scanner over.
"How's Kaidan anyway?"
"He's fine I just re-adjusted his L2 implant in the hope I could fool the guard." She walked behind Garrus who carried Kaidan towards a corner of the room. "This injection should wake him up, he will take a few minutes. What about the meat pile?"
"James remember him? He was drugged on a gurney in the infirmary. Dozes off again every few minutes." Garrus carried John over towards the operating table.
She turned towards John studying over the scans she made.
"He's fine for now, but someone messed around with his implants. We can't do anything but wait until everyone is back on their feet. But tell me why didn't he know who I was?"
"Amnesia, is all I got for you. The details well that's why we have been searching for you actually." Garrus set up a defensive position in front of the doors.
"By the looks of his brains someone tried to actively mess with his memories."
The alarm on John's omni-tool beeped for a short moment.
"Liara we haven't heard from them in 35 minutes, the distress signal came 5 minutes ago. We should call the council and ask what to do. Hell we even lost EDI before that. I'm worried Liara."
Liara stood in the CIC next to Traynor. "Anything?" But she already knew the answer.
Traynor just shook her head, seemingly disappointed that they couldn't establish contact.
"Steve any sign of them out there?"
"Negative, can't fly near enough anymore the towers are manned. They set up turrets a while ago."
"Damn, Traynor connect me to the council. We will need help."