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.
Surrendering
Kaidan had run down towards the bar to grab a bottle of Whiskey. He stood slightly out of his breath back in front of John.
"2 minutes and 42 seconds, how did you do that?" John had stopped the time on his omni-tool.
"I threatened EDI to cut power to her Humor heuristics if she didn't speed up the elevator for me."
John lifted an eyebrow. "Really?"
"Nah, I just called it a spectre priority mission." Kaidan grabbed two glasses. He was set on making John comfortable again. Kaidan would have preferred to just grab John and kiss him until they couldn't breathe but he knew it wasn't the right thing to do. No matter how much he longed to finally be with John, his own feelings would have to wait. But as long as John wasn't even comfortable with himself Kaidan didn't want to push anything that could complicate things.
"So what did you get me?" John took one of the glasses.
"Honey flavored Whiskey."
"So a toast?" John waited for a second to see if Kaidan would interrupt him. "To freeing a lot of civilians and crossing Cerberus' plans once again."
"I'll drink to that." Kaidan lifted his glass and took a big swill.
"Great drink, the one good thing about amnesia. I get to rediscover all these tasteful drinks and foods." John grinned slightly as he looked towards Kaidan.
"So what's with you and Charles?"
"Well he's been helping me with the control chip. He had this idea that if we train it often enough I could be able to prevent someone from using it against me." John rubbed the back of his neck. "Also it seems Cerberus had not yet unlocked the full potential of their toys." John filled up their glasses again.
They talked like what had seemed for hours, until the bottle was empty. At some point John had noticed Kaidan had dosed off curled up on the sofa. He picked him up and laid him down in the bed, removing his boots and tucking him in before he slipped in beside him. John brushed a lock of hair back from Kaidan's forehead. "I really like you Kaidan, I wonder why the old me didn't see you the way I do now." He whispered more to himself as to anyone else.
Hannah had a horrible headache, she could barely remember what happened last night. The smell of fresh coffee spread across the room, Emma was probably making breakfast for everyone. Hannah had to admit that finally getting out of her military life for a few days was a much-needed distraction. Even if there was a whole unit of marines here to secure the perimeter.
It had been a nice surprise that the Lieutenant here was the daughter of one of her old CO's. But it also made her suspicious about what exactly Major Alenko was doing. Luckily today she would find out more, the major was coming over and since they where far away from the Alliance and the council maybe he would have something more to say this time.
She went towards the kitchen where she saw how Emma was already set out a plate and a cup of coffee.
"Aspirin is on the counter, scrambled eggs and bacon should take care of the rest." The woman just said while she came over with a large pan full of eggs.
"Gosh how much did we drink yesterday?"
"Me not so much, you on the other hand a little more." Emma smiled while she grabbed herself a fresh bread bun.
"When is the Major coming?"
"Kai said they be here in the afternoon. So we have plenty of time to get you straightened up and start backing that apple pie we talked about."
"Emma, I told I have no talent for baking. I spent my life on ships we get dry-freeze meals."
"See time to change that and it's easy." Whit that Emma had ended that topic, Hannah knew the woman would make the pie anyway. She had seemed excited after the major had called her yesterday.
"So explain this to me again, my mother is a rear-Admiral in the Alliance and the Human Councilor?"
"Yes and at the moment she is visiting my mother."
"Okay and this is at the place where I got in a fire fight with a bunch of alliance marines when I was told to kidnap your mom." John had asked Kaidan at least 3 times since he was told where they were going today.
"Yeah but that was before. Anyway we are almost there.
John felt uneasy at the thought of meeting his mother, especially since she believed he was dead.
The shuttle landed on a field on the other side of the orchard. He could smell the sun on damp earth, feel the soft breeze.
Amidst the trees they got stopped in their tracks by a marine in full combat gear. "Identify... Oh Major Alenko we weren't expecting you so soon."
"Lieutenant Smith, how's the job here going?" Kaidan was happy to see that the Lieutenant was still stationed to protect his mom.
"Other than that we now have a councilor to protect and a Krogan who's bored because nothing ever happens? Really good I guess." The woman nodded towards the house. "Cleanup went smooth, the Salarian spectre though... Well lets say he was really secretive after he was done."
"I can only guess why he would do such a thing Sandra." John interrupted as he walked towards the marine.
"Shit, Johny? No way... But you're dead." She barely got the words out.
"Yeah, the report of my death was an exaggeration." John smiled at her.
"Damn Johny I saw your funeral in the vids. How in hell did you survive?" The woman fell in John's arms.
"Hey the Alliance has been wrong before... You really think they can get my death certificate right this time?" John held tight to the female, in his mind she was still a girl from his past but he recognized her the second he saw her.
Lieutenant Smith pulled away. "You should get to your mom she is waiting... She doesn't know does she?"
Kaidan cleared his throat. "Johny? Really?"
"Yeah Major. I dragged his ass through boot camp. My kind of payback for breaking my heart."
"Yeah and only she gets to call me that. We spent years together in the Alliance after we cleared up why I wasn't in to her." John grinned following her gaze towards James.
"Say Lieutenant, I bet my mom made a whole lot of Pies today. Why don't you come by later and you get to tell us everything about John's early years."
"Maybe I will, Major but I have to get back to my duties for now." Sandra nodded her head towards the group, John noted that her gaze lingered a bit longer than normal on James.
As they proceed towards the house john suddenly spoke. "Say James what do you think of the Lieutenant back there?"
"You mean the hard-core marine that fills out that armor in all the right spots... Man you must be Loco to turn her down."
"Not my type, you should talk to her. Think she likes you." John's gaze fell upon Kaidan.
"Wouldn't know what to tell her Loco."
"Ask her about what happened after her date with me... She loved to tell that to anyone who would listen."
They had reached the house. Kaidan paused a second before he knocked on the door. It didn't take 3 seconds before he heard the familiar voice of his mother from the inside. "They're here."
The door flew open and the small woman flew around kaidan's neck. After a few seconds of hugging her son the woman stood back. "Kai, you never mentioned your commander is a looker."
"Eh mom!" Kaidan's face turned a few shades of red darker.
John stepped holding out his hand. "Ma'am a pleasure to meet you. I'm John Shepard but please just call me John."
"Well Kai, why don't you take your friends over to the kitchen. I made your favorite, Apple Pie." The woman hurried back in to the house.
"So Major Kai huh?" James chuckled from behind.
"Shut it Burrito."
"Hey that's mean. Guess I'll have to tell scars about Kai and Johny here." James got knocked back when both biotics simultaneously unleashed a small biotic field on him.
"James you better get out of here, go and fool around with Lieutenant Smith." Kaidan said while he grinned towards John.
John already smelled the freshly backed pie, his nose had led him to the table where a big pie was still cooling off. The table was set and Emma already brought a can of coffee towards the table.
"Where's the councilor mom?"
Before she could answer John heard footsteps coming down the stairs. A small notion of panic came over him, maybe he should leave while he still had the chance.
But he stayed, Kaidan looked hopeful over to him before stepping in to the hall. John could hear them talking.
"Ma'am, before you enter the kitchen there is something I need to tell you." Kaidan's voice was just a slight bit unsteady.
"Major I hope you have a good reason for not telling anyone what the hell you've been doing." The female voice was soft but determined.
"I have, now please believe me i saw no other way to solve this but you have to meet someone."
The woman stepped in to the room Kaidan following her looking hopeful towards John.
"What the? This can't be..." The woman's jaw dropped her eyes wide open.
John gathered his thoughts before speaking. "I was told you are my mother, I'm sorry to say I can't really remember much of my past."
"Kaidan is this real?" The woman looked over her shoulder.
"Yes, it's really him."
"But the body, everyone was sure it was him." Hannah seemed to grasp for explanations.
"From what I understand there where clones after my last resurrection." John frowned a bit.
"There is only one person who could have identified his corpse, Mirada Lawson she rebuild the first time. But we can't find her." Kaidan walked over to the table pulling out a chair for Hannah.
"So how can you be sure it wasn't him after all?" Hannah sat down the shock was still visible on her.
"At first it was only a hunch, something was missing. But after meeting Aria, well everything became clearer." Kaidan cut the pie and gave everyone a piece. His mother had tactfully disappeared. Wile they talked about everything that had happened.
John had left Kaidan and Hannah, he really didn't know what he could do since they moved on to politics and strategies.
The sun was slowly dropping towards the horizon. In the sunlight he saw Emma sitting at a bench between the trees.
"Miss Alenko, Everything alright?" John sat down next to her.
"Yes I'm just remembering how I used to watch the sunset with my husband right here on this bench."
"Did he?"
"Still MIA, but the Alliance is putting forward a notion to declare everyone who's missing death by the end of the month."
"I'm sorry." John starred at his feet.
"Don't be, you and your crew did so much to save us all. I believe my Richard would have been proud that his son was there with you."
"I didn't save anyone. That was all the other me, I can barely remember that there ever was a war."
"Don't worry about it, one day you will remember what's important. The other things? Who cares, as long as you're happy it doesn't matter who you used to be." Emma leaned back a bit enjoying the last sun rays on her skin.
"I guess your right, Just... Ah it's complicated." John dropped his head in his hands.
"Is this about Kai undressing you with his eyes?" There was a slight amusement in her voice.
"I.. Eh what... How.. NO!" John's face turned red.
"So it is about that, well where is the problem?"
"Just, I don't know. Did I love him before the Amnesia thing and if yes then why did I turn him away." John's voice was close to cracking.
"I'm going to tell you the same thing I told Kaidan a few months ago. Go for it, tell him how you feel, He'll understand. If you don't talk to him you'll never figure it out." Emma stood up. "Wait here I have an idea how to solve this."
John sat there alone for a few minutes just watching the sun go down. A hand dropped on his shoulder.
"My mom told me I needed to bring you this." Kaidan held out a bottle of red wine and two glasses. "Also that you wanted to talk with me."
"Yeah, I think she tricked me into this..." John took the bottle from Kaidan.
"She is very manipulative like that and whenever she sets her mind on something no one can stop her." Kaidan held out the glasses for John to fill. "So what's so important that my mom saw the need to trick you."
"We'll crap this isn't easy... It's just... I don't know how to..." John stared on a point between his feet.
"John... Look up." Kaidan's hand lay gently against john's cheek, slowly forcing him to face him. "Whatever it is just talk to me, I can handle it."
"I'm not sure how to put it, I'm afraid that whatever I feel isn't real and might change in time." John took a deep breath.
Kaidan took both their glasses at set them down on the bench before standing up and pulling John to his feet. His hand moved to the back of John's head forcing him closer with a slight pressure.
When their lips met the sun behind them slipped under the horizon. After a moment Kaidan loosened his grip so they both could breath. In the corner of his eye Kaidan saw the Shepard from his dreams smiling, when he blinked the other Shepard was gone.
"You where saying?" Kaidan whispered.
"I'm afraid, Kaidan what if I regain my memory and everything changes?" John's voice was hoarse.
"It wont change anything, believe me this is meant to be." Kaidan thought back at the strange dreams he had had. Everything in them always came true.
John surrendered to his feelings. "To hell with all the doubts." His words sounded a bit more playful now. Suddenly Kaidan could feel Johns arm on his back holding him. John's head lowered, playfully his tongue darted over Kaidan's lips. It didn't take long before they where once again kissing this time more urgent, a more basic need for each other, teeth clacking together tongues intertwined.
Somewhere in the back James stood with three woman sharing a bottle of wine. Lieutenant Smith nudged James' side with her elbow.
"So Girls who had money on they won't even drink the wine?" Sandra spoke cheerfully.
"That would be me Marilyn." James nudged her back in the side.
"Geez, how could you have guessed that one anyway James?" She paid out the pool.
"Ha, there is one rule on the Normandy." James grinned as all three looked straight at him. "Never bet against the Commander."
The tree woman all started laughing at the same moment. "Damn James you could have saved us the trouble of opening a bottle for them." Sandra hit him on the shoulder. "Now move your fine ass marine, we should leave the lady's alone, we grunts belong in the dirt."
James Saluted her. "Yes Ma'am, in the dirt ma'am." He chuckled slightly as he walked of with her.
Hannah took a sip of her wine. "Damn over three years, a reaper invasion, possible multiple deaths and all it took for John to open up to someone was a case of Amnesia and someone to pin him down?"