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.
Amnesia
Shepard hadn't even hit the floor before Karin leapt in to action. The Doctor grabbed a bag from under the bed, preparing her medical gear. "Kaidan tie his hands together, Shepard has a higher tolerance to tranquilizers then normal men." She stopped the bleeding from the gunshot wound in John's arm and set her omnitool to monitor his vitals.
Kaidan pulled of the helmet from John's face, revealing the bright red glowing eyes and scars. "Damn what had those bastards done to him?"
Karin shook her head. "Looks similar to the first time I saw him after Cerberus rebuild him. But I can't say anything for sure until we get him properly examined."
"Cortez, bring in the shuttle we need to get target Sierra to the Normandy." Kaidan waited till he heard Steve confirm that he was on his way. When the shuttle landed he picked up Shepard and wrapped a blanket around the man, Carrying him to the shuttle.
"So it's really Loco?" James waited outside.
Kaidan saw Lieutenant Smith coming nearer, the woman walked with a determination straight towards Kaidan.
"Yeah it's Loco. James I want you to go with Doctor Chakwas back to the ship. Guard Loco in case he wakes up." He gave James a little nod towards the Lieutenant coming their way.
James pulled the blanket over John's face and carried him away to the shuttle.
Kaidan straightened up when the Lieutenant stood before him.
"Major, the area is secured. My men will patrol the area for now. Shall we send in someone to clean up the house."
"Good and don't bother with clean up, we have a special crew for that." Kaidan pondered a bit, he should remind Jodum Bau not to torch the place this time.
The lieutenant shifted her weight from one foot to another. Clearly she was considering to ask him something else.
"Lieutenant speak your mind."
"Sir, it's just... Well we don't really know what we should write in our report to Alliance command. We where here because the Shadow Broker pulled a few strings. But we still have to report our actions."
Liara cleared her troth coming out of the house. "Lieutenant, don't worry about it, I asked for the Brokers assistance. I'm sure your Alliance will get a satisfactory explanation."
"Liara why did you pull in outside help anyway?" Kaidan wondered about the lieutenant's presence.
"When we arrived here, it became clear that there where far to many civilians Styx could use against us. I thought replacing them with marines was a good idea. But I couldn't risk contacting the Normandy as long as the bugs might still be active. So I pulled in a few favors, being part of Shepards team throughout the war has granted us some favors."
"Good call Liara."
When the Lieutenant had left Liara whispered. "And she knew Shepard from boot camp, they are old friends."
Kaidan took a deep breath and typed a message to his mother. Telling her she could return in a few days.
"So explain this to me, you really tried to hook your son up with your CO's daughter?"
Hannah's smile grew broader. "Yeah, not one of my finer moments. I really thought John finally needed to go on a date. He was 17 after all. So I convinced him to take the girl out. It didn't end like anyone could have expected."
"Wait what did your CO think about that?"
"Oh Captain Smith was fine with that. Well at least right up until the point when his daughter came back from the date." Hannah laughed when she remembered that day. "Next thing I knew I ran in to the Captain chasing after my son threatening to beat him to pulp."
"Wait what did he do to the girl?"
"Nothing, but the Captain had only seen how his daughter came home crying and assumed the worst. So anyway, I see John running away up until he was cornered, the Captain grinning and rubbing his fists. Suddenly the captain flew several feet backwards. That was the moment we discovered John was a biotic."
"I think I prefer my son letting his toys levitate to levitating a Captain." Emma chuckled.
"Yeah the Captain was so shocked from the experience he completely forgot why he was angry."
"So why was he angry in the first place?"
"Hah, turns out the girl had a crush on John. When he didn't make a move she tried kissing him. John hadn't reacted to well to that. Apparently the girl was, how did he put it... Annoying"
Both woman where laughing, when Emma's omnitool beeped. "Kai how is it going?"
"Ugh mom, I'm assuming you aren't alone?"
"No, the human councilor and I are just exchanging embarrassing childhood stories from our sons."
"Okay, then it's probably a good thing that the mission went as planned, a team will clean up the house. But your good to return home."
Kaidan was happy to finally be on the Normandy again, Jodum Bau was taking care of the Orchard and the Alliance was still in the dark about John.
Kaidan didn't bother stowing his equipment, leaving everything in a corner of the shuttle he stormed off to the med-bay. He had to know how John was doing. Now that he finally had the man back he wasn't going to leave him again.
Kaidan was prepared for a lot, but not for the sight of Charles, EDI and Glyph around the body of what he assumed was Shepard. The three where hard working on something while Doctor Chakwas was sitting in a corner looking over some medical scans.
"Ehm, hello anyone?" The trio didn't seem to notice Kaidan entering.
"Oh, Kaidan you're back. Suppose you want an update?" Chakwas turned around to face him.
"What's up with those three?" Kaidan nodded in the direction of the three synthetics.
"Charles is interfacing with the implants in Shepards head, EDI and Glyph are assisting him. Something about more processing power when they work together."
"They are what? Why?"
"Kaidan it's problematic. Physically there is nothing really wrong with Shepard, at least nothing serious. Just his brain is wired up to a control chip. We don't know if we can remove the thing without risking permanent brain damage. So Charles is trying to find out what was done to him exactly and if he can disable the chip without damaging Shepard."
"But if we disable it he will be himself again?."
Glyph hovered over towards Kaidan. "Major, we can download some of the data on the chip. Disabling is to risky for now. Charles offered to store Geth in the device to shield the commander from outside influence."
"Wont that just give the Geth control over him?"
"Yes, but it's either that or we have to keep the commander sedated until we find a way to extract the device."
"Shit I really hope we won't regret this, do it." Kaidan didn't like the idea to giving Shepard over to Geth control but it seemed at least better then letting Styx do whatever they where doing up till this point.
Charles turned away from shepard and walked towards the AI core. "We are now interfaced with Shepard, his vitals are stable, his thought processes are confusing. We should take time to consider this new information."
Glyph bobbed in the air. "Doctor Chakwas, You can take him of the sedatives."
"Thank you Glyph, ask Liara to search for more information about this type of implants."
Dr. Chakwas moved over and removed the infusion from John's arm. Checking up one last time on his vitals she shrugged and turned. "He wont be up for several hours, there is nothing I can do for him at this point. I'll call you when he wakes up."
"No i will wait here. I.. I.. Just.."
Karin nodded, a small smile on her lips and left the med-bay. He could hear how she talked to James who was sitting in full combat gear in the mess hall.
Kaidan sat on a bench between the trees, the sunlight was shinning through the leaves playfully dancing on the grass as the leaves moved softly from a slight breeze.
He remembered how he had sat here on the same bench on the evening before he enlisted. That evening he had spent at the Orchard with his mom crying, not wanting him to leave and his dad proud that his son would follow in his footsteps.
He heard soft footsteps falling on the grass beside him, slowly turning he looked in deep blue eyes. The eyes that could only belong to John.
The man sat next to him on the bench smiling at him.
"So, you didn't give up on me."
"You knew I wouldn't" Kaidan felt pure happiness when he looked at the man he loved.
"Kaidan. You might have stopped me from going, you might be pulling me back. But I'm still lost in here."
"Yeah about that... John what is here?"
John bent over laughing. "No idea, but it's always more beautiful when you come and visit me."
"Wait John, are you saying this isn't a dream?"
"Hell if I know, but who cares we are here now." John wrapped an arm around Kaidan. "What do you say we just sit here and enjoy the view."
Kaidan grabbed John's hand. Holding tight never wanting to let go.
The sun disappeared under the horizon and he felt Johns hand hold on a bit harder then before.
He woke up disoriented, where the hell was he. He tried to remember, there had been a fight. Someone had drugged him. The Whispers where gone, normally there should be whispers telling him what he needed to know but nothing... There was only an empty silence.
He became suddenly aware of a hand holding his, the hand belonged to a man sleeping beside him. He squeezed the hand. The man woke up, raising his head smiling. "Brown eyes" he gasped. He remembered brown eyes, he had been there at the end of the fight.
"Hey John feeling better?" Brown eyes said in a sleepy voice.
He wasn't sure how to react, no voices to guide him, he was alone in an unknown place no armor or weapons. This didn't look very good. "Who's John?" His voice sounded raw.
"YOU HAVE WHAT!"
"We have lost Deimos sir."
"What the fuck, how do you lose someone like that? Trace him, I don't care how you do it, just do it."
"Yes, sir we will do everything in our power to find him."
"It would be better for you and your team, we don't have use for failures."
"Yes sir, we understand."
Brown eyes had gone outside with the doctor to talk. They had left him in the med bay with a marine they had called James.
"So ehm, James was it? What did you do to get guard duty?"
"Shit Loco you really don't remember? Man that's just..."
"Why call me loco? The Krogan called me Shepard and the Major called me John."
"Damn Loco, you now it's because you're all kinds of crazy. Just a nickname."
John tried to remember, but there was nothing.
John closed his eyes waiting for Kaidan to come back something about him was reassuring, giving him the confidence that he would find out how everything fitted together. If he concentrated a bit he could hear a conversation somewhere on the other side of the door.
Kaidan was getting angry, he couldn't believe what he was hearing.
"Look Kaidan all I'm saying is that his memory might already be permanently damaged. We don't know if he can ever recover. The decision what to do should be with his next of kin."
"Karin with all due respect what do you think the Alliance will do to him? Last time they locked him up for half a year, this time there will be no reaper invasion to get him out. Not to mention if they ever find out about Admiral Anderson."
"I know Kaidan, but he's a spectre after all and the savior of the whole galaxy. Not even the Alliance bras would risk an incident locking him up."
"Yeah about that, last time I checked his Spectre status was removed the moment he died, not to mention that they already had his funeral for the second time. Just give him some time to recover, at least give us the time to find out who did this to him before we tell anyone he's alive."
"Fine, but we really need to find him an expert, someone who can tell us more about these new implants." Karin gave up, Kaidan wasn't going to give up.
Kaidan spun on his heels and opened the door to the med bay where john sat up the moment he caught sight of Kaidan.
"So this the part where you're gone lock me up?" Shepard shrugged. "Because that seems to be the story of my life." John pointed towards James. "So he's gone be my watchdog?"
"No, as soon as the doctor clears you, you get to move back in your own room." Kaidan pointed towards the ceiling.
"In fact you can leave latter this night, I just want to do a final checkup. But I will have EDI monitor you for the next few days." Karin was already moving her gear in position.
A few hours later Shepard was standing in front of the elevator. The doctor had told him he could move around the ship freely but he would be monitored through the internal security system. But no one had mentioned to him where his room was. John was considering where he should start to search for his room, would he even recognize it if he found it?
Suddenly a disembodied voice spoke. "Shepard can I be of assistance?"
"Ehm, I was told that i could go to my room, but I don't know where that's supposed to be. Oh and who are you?"
"I see, I'm EDI the ships AI. Your room is on the first floor, Shepard if you need further assistance just speak to me from anywhere on the ship. Also my platform is most of the time in the cockpit with Jeff, my personal slave." She paused for a moment. "That was a joke. Jeff is the pilot."
"ehm tanks EDI." A ships AI making jokes? Just on what kind of a ship was he. John pushed the button to the first floor.
John was taken aback, he had thought that they had given him some small room, maybe something more like the glorified cell Phobos had appointed him to. But this room was huge, damn the whole purpose of the first floor was this room.
"Ehm EDI? Is this some kind of joke?"
"No Shepard these are your private quarters, They have been since the ship was build."
"Your kidding, whose ship is this anyway?"
"The Normandy was under different designations. But she has always been yours Shepard. The Normandy and myself where created for you."
John walked over to the fish tank, pushing the button to feed the fish. He smiled seeing the collection of fish dart up to reach the food.
Kaidan and Dr. Chakwas sat in the AI core watching John's reactions. "Did he just feed the fish?" Kaidan asked.
"Yes, his neurological reaction seems to indicate he likes the fish, though it's hard to tell he remembers them or just automatically assumed they needed nourishment." Charles answered.
Karin shook her head. "Nah that smile, he might not now it himself but he remembers something about the fish. You should have seen him whenever the little buggers died on him."
"It still feels wrong to just leave him on his own." Kaidan's voice broke away.
"It's the best way, if we all go and bother him with facts of who he used to be he might not be able to process it himself. We only answer when he asks and don't worry Charles can warn us if he has problems."
Kaidan nodded, it would be hard not to run up to him and tell him how he loved him. But John had to find out who he was first, Kaidan would wait for him. Waiting was a lot more easy now that he knew he could see to John's safety.
Note: I've had a lot of strings to clear up after the last chapter, which proved more difficult to write then I imagined.