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.

Epiphany

When Kaidan arrived on the Normandy EDI was already waiting for him. She came towards him and held something in her hand.

"Kaidan, the Normandy was bugged. Someone has been listening in on us."

"Shit, you caught all bugs?"

"We think so, the devices where centered on the Med Bay and the mess hall. Going from the logs it is reasonable to assume that the refugees you picked up at Arcturus where Styx operatives."

"So the attacks, everything was because they knew?"

"Probably... Yes." EDI cocked her head, it was astonishing how she behaved more and more like a human.

"So ehm how did you find those?" Kaidan pointed to the devices.

"We didn't Charles did. He is currently in the AI core, Kaidan you might want to talk to him."

Kaidan nodded "He is repaired?"

EDI smiled. "Yes, Kaidan you're the only organic that calls him 'he' instead of 'it'."

Kaidan shrugged "EDI, you're a individual , Legion became an individual near the end. If we don't accept them now as individuals after we reactivate them, then how can we ever see them as equals?"

EDI smiled "Thank you Kaidan. You will never understand what it means to hear that. You should go and talk to Charles he refused to talk about what happened without you."

"I'll go as soon as i can, need to look in to something first.

Kaidan went to his locker and dropped of the care package his mom had given him. He planned on having a nice dinner with his friends later that day.
Kaidan went to the Med Bay, he was sure he could get the help he needed from DR. Chakwas.

"Kaidan you're not feeling well?"

"I'm good, i just wanted to ask you something."

"Okay, what's wrong, you would never come here of your own free will."

"I just wanted to ask you to run a DNA analysis on this sample here." Kaidan handed her a piece of glass with a blood stain on it. "Also do we have any medical data about experiments that gave humans red glowing eyes?"

Katrin looked chocked. "Where did you hear about that?"

"I didn't hear anything, just this one Styx mercenaries his helm got cracked. He had these strange red glowing eyes, almost like the blue indoctrinated Cerberus people. The guy behaved really strange."

Katrin pulled up an image of a pair of red eyes. "Did they look like those?"

Kaidan couldn't believe it that where the exact same eyes he had seen yesterday. "No they didn't look like those, they where exactly the same. Where are they from?"

"The Normandy medical records. Sealed personal files, from back when Cerberus ran the show. Kaidan those are Shepard's eyes."

"Wait, Shepard had blue eyes." Kaidan couldn't believe what he was hearing.

"He used to yes, but those red ones are from his implants, He spent a huge amount of resources, So they wouldn't be visible. Used to be you could see the same red glow through his scars."

"That would mean the mercenary had the same kind of implants?"

"Likely yes, I'll run that analyses if you don't need me for anything else, shouldn't take too long."

"Okay thanks, i need to talk to Charles anyway." Kaidan nodded to the AI core.

Wen he entered the AI core Charles was doing some strange dance moves. When the Geth noticed Kaidan enter he stopped.

"Alenko Major, I.. We are sorry about the way the fight went."

"It's okay Charles and hey i beat the odds you gave me." Kaidan grinned.

"Alenko Major, we seem to have miscalculated the Garrus Paradox, we will adapt our calculations from now on." The plates around the head light shifted.

"EDI said there was something we needed to talk about?"

"Yes, when we where in combat, an anomaly held us from taking action. Our higher runtimes could not reach consensus about a ... conflict that arose."

"Okay Charles what conflict?"

"Alenko Major the designated enemy, was a ally of the Geth. We never before had to face a conflict this one."

"Okay, so do you know who this ally was?"

The Geth's head cocked slightly to the side, plates moving as if he was pondering.

"It appeared to be Shepard Comander."

Kaidans head spun, he felt dizzy. The whole universe slowed down in that moment. The Geth must have made a mistake, it was impossible. Kaidan had to sit down, the Geth don't make mistakes like that. But the idea it was just no... I must be another clone or someone who just looked like him. Kaidan felt miserable.

Charles had watched how Kaidan sank to the floor, he noticed how the humans hart rate increased, his breathing became rapid ."Alenko Major, you are Hyperventilating. Do you require assistance?"

Suddenly the world stopped spinning. Everything was peaceful, warm and beautiful.

Kaidan stood on a field the grass was just a bit greener then it should be, the sky a hint more Blue then usual. He looked around, the field had a great view of English Bay. A bit further ahead he saw a bar, no not a bar. The same bar where he had been yesterday. Shepard sat at the bar holding a glass of blue liquid.

Kaidan walked over, no he thought he walked but before he even started to move he suddenly was at the bar.

"Kaidan have a drink, I've been waiting."

Kaidan looked in to the face of the man he loved. Blue eyes, not red. "Why are we here John?"

"No idea, Kaidan. But it sure is nice here isn't it?

"John, was it you who we have fought?"

Shepard looked down at his glass. "You already know the answer Kaidan."

"No, i refuse to believe that you would do such a thing."

Shepard shook his head. "Kaidan it doesn't matter anymore, I told you I was gone. You have to let go."

"I can't, I have to.."

Johns hand went up to kaidan's chest. "Kaidan the only reason I'm still here is you, You want me to be here so I am. But I'm gone. This is all that's left."

"Be honest would you give up if our places where reversed?"

John pondered a moment. "No, I wouldn't have given up on you."

"Then don't expect me to."

John stood in front of Kaidan pulling him in for a kiss. "You have to live your life Kaidan, just take it one day at a time."

"Kaidan?" I believe he is awakening.

"Who what, no not again." Kaidan's vision cleared up. He was still in the AI core. Directly in front of him was DR. Chakwas.

"Kaidan you seem to be fine, only your brain activity seems a bit off, but otherwise everything seems okay. So I have to ask why did you say again?"

"It's nothing just dreams." Kaidan felt sorrow, why did the dream always end just that little bit to soon.

"Okay, but you might want to talk about those dreams you're having. Your biometrical readings in the last weeks have been troublesome."

"Really it's nothing. I'm more interested in that blood sample I gave you Doctor."

"About that, may I ask where you got that?"

"From the funeral, why?" Kaidan didn't dare to get his hopes up. It must have been John.

Doctor Chakwas looked uneasy. She clearly didn't want to voice what she thought.

"It's John isn't it?" Kaidan could barely hold his voice steady.

"Yes, but you already seem to know that. So where did you get that blood Kaidan?"

"I told you about the Mercenary with the red eyes. He shot himself and ran of, behaved really strange. Anyway the blood is his. After Charles said he saw Shepard during the attack on the labs it just made sense."

"Kaidan we have to inform the council. His mother should know."

Kaidan shook his head. "No, we have to find him first. But next time we will be prepared." Kaidan typed a message in his omnitool.

Kaidan sat in the mess hall that evening, trying to stomach the horrible coffee the Normandy served.

"Geez Kaidan are you drinking that or do you just want to be holding on to something hot for a change?" Joker grinned.

"The coffee just reminded me about mom, she's all alone now. I just hope she doesn't get lonely on the Orchard." Kaidan looked at his hands. "Since dad is MIA, I don't know, she just seemed so happy to see me."

"Yeah you told me about the pancakes about 10 times in the last few hours. Geez Kaidan, she will be fine, if something happens she'll call you."

"Yeah sure but still, she shouldn't be there alone. But she didn't want to leave."

"Stop worrying Kaidan, let's do something fun for a change. I hear Garrus is challenging James tonight. A friendly sparring, I so want to see James getting his ass kicked."

"Yeah you're right I need to stop worrying."

Both men walked to the elevator, Kaidan had a hard time keeping his expression neutral. EDI waited inside the elevator.

"How did it go?"

"Good."

"Deimos, I have a special job for you."

"What's up Phobos? Anything on the traitors?"

"I think we might have a way to lure them out. We just received news that someone close to their leader is on earth. Our agents are closing in on the position as we speak."

"You're sure they will show themselves?"

"In this case we can be pretty sure. I want you to prepare a team, it could be beneficial if we set up a good trap to finish them off once and for all."

"Thanks Phobos, I should go."

He couldn't believe it, finally he would be able to catch the traitors off guard.