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.
Cover Up
Garrus ran through the corridors, coming to a stop wen he turned the last corner.
The dust had started to settle but everywhere he could see the damage the explosion had left behind.
"Kaidan? " Garrus yelled through the corridor, readying his weapon just in case the mercenaries where still around.
"Garrus is that you?" A familiar suit bent around the corner.
"Tali, spirits you're okay. " Garrus ran over until he was in front of her. Quickly wrapping his arm around her and pulling her in a tight embrace. "Have you seen Kaidan, he should have been here somewhere."
"Kaidan is fine, he got knocked out, but nothing serious"
"and Charles?"
"Who's Charles?" Tali cocked her head slightly.
"Ehm, the Geth I mean."
"Killah, sent a Geth for a minute to the Normandy and someone is bound to give it a name." Tali's hand went to her face, shaking her head in disbelief. "Yes the Geth is here, it got fried though the mercenaries set of some kind of EMP explosive before they ran. I was able to recover his memory core but we will need to fix the platform before trying to reactivate him."
"Good he seemed nice and he might have some more intel we could use. Lets get the Geth and Kaidan back to the Normandy."
"Kaidan!"
"Shepard, am I dreaming again?"
John looked sad. "I'm so sorry Kaidan."
"What, why are you always apologizing?"
"Kaidan please, just forget me. I'm gone. There is nothing left."
"No, shepard I must find you. I must..."
John shook his head. "Kaidan it's too late. You could never have reached me in time, it just wasn't meant to be."
"No! I wont give up. I must find you." Kaidan couldn't believe it, how could Shepard be so stubborn.
"Kaidan you where always way to stubborn for your own good. Forget about me it's to late. I'm gone."
"NO! I wont accept that!"
Shepards face was wet with tears. "Kaidan you need to give up on me or you won't survive it. You know it."
"Shepard I can't. I will never give up."
"You know I'm gone Kaidan. Just think, you already know it. Now just give up, it's over." Shepards hand moved to Kaidans chest resting where the ring hung on it's chain.
"I love you Kaidan. Farewell."
"NOOO..." Kaidan sat upright. What the fuck?
"Hey sleepy" James sat on a chair next to him. "Really half of the time I see you you're knocked out, should call you sleepy from now on." James had a grin on his face.
"What happened?"
"Sure hopped you could tell us. We have been keeping watch next to you. The Doctor said you just got knocked out. So eh what's with the yelling NO?"
"Ehm, nothing just some bad dreams." Kaidan wasn't going to share something so personal. "So, the council?"
"Safe, have them onboard till the destiny ascension is secure again. Hacket was pissd about us going dark, but happy we kicked his ass out of the crap he was in."
"Tali?"
"Oh sparks? She's onboard again, patching up our Geth friend he got fried a bit after some explosion. If you're up to it we can have the debriefing. Though you can just pretend you have a migraine or something. Don't think the debrief will be fun with an Admiral and the council onboard."
"Hacket is onboard? Did he find out about Anderson?"
"Nope Liara took the stasis pod to her chambers. No one gets in there without her permission, Glyph has fun playing the bouncer, guess the little VI took lessons from Grunt."
"Thanks, i should really rest some more. Tell the others the debrief won't happen before tomorrow." Which would also give him extra time to make up a cover story.
"Sure, I'll inform DR. Chakwas that you wanted to sleep some more. You might want stick to the sickbay though. With the ship full of important people."
"I'm not always up in Shepards room!"
"No only whenever you're sleeping. Kaidan we have an all seeing AI onboard remember?"
"Damn EDI they could just ask her anything."
"Don't worry Kaidan, Liara took the liberty of locking my mission logs. She made a serious case that it fell under a Spectre confidentiality protocol I didn't even know existed." EDI's disembodied voice sounded over the med-bay speaker.
"Okay thanks EDI. James." Kaidan nodded and laid back on his bed. A few hours of sleep would really help.
Kaidan woke up hours later, the Normandy was silent only a the engine hums where to be heard.
"EDI what the time is it?"
"We are currently at 3:15AM standard sol cycle."
"The councilors and the Admiral where are they?"
"They are in the crew quarters, asleep."
"Thanks EDI." Kaidan sat up he wasn't tired anymore might be a bit early but now was the perfect time to catch up on reports and Intel before the debriefing took place. Also he really needed to invent a believable cover story for their mission.
Kaidan walked out of the Med bay and made some coffee and breakfast. Like every morning he got annoyed by the horrible coffee that no matter how you made it always tasted burnt. Okay it kept him awake but the stuff was disgusting.
He loaded the reports from the attack on a data pad and read through them. A lot of ifs and maybes in those reports. He would need Liara to solve this. Kaidan walked over to Liara's room wen he was about to knock on the door it just slid open.
Glyph hovered in front of him "Hello Major please come inside."
"Ehm Liara awake?"
"Here Kaidan" She sat on her bed between a pile of reports. Next to her was the stasis pod.
"Geez why are you up so early or is it late?"
"I could ask the same about you Kaidan. But no it's early, just wanted to work on these reports before the council wakes up."
"Yeah about those i guess we need to make up a cover story about what really happened on the citadel now."
"Already done. We only need to cover up two details. The part where we have Andersons body and the part where we actually saw the area. Aria has seen to it that another room had a little explosion. The new version is simple we came to late, the mercs had stormed the place and set of an explosive device there was nothing left and Andersons body is nowhere to be found. We went dark to search who was behind the explosion. Accidently the same merc group who attacked the council."
"Ehm you sure they will buy it?"
"Sure, no one is allowed near the presidium at the moment. Plus we have footage of the burned out and utterly destroyed room. Even has an image of a dead burned merc body."
"Wait she didn't?"
"No Kaidan they just took one of the dead mercs you encountered and placed him conveniently there."
"How did you get Aria to cover us anyway?"
"Nothing special, I mentioned Bailey could be taken in for questioning if the Alliance found out what happened, Also I might have mentioned that my father is the new Asari councilor."
"So she and Bailey huh?"
"I wouldn't say anything, but she likes having him around for some reason." Liara grinned a bit.
"About yesterday do we have to change anything about that?"
"No the truth is we have not much to go on anyway. But Kaidan something feels wrong about all of this."
"What do you mean?"
"Well first the citadel, if someone near the council or Alliance command had told Styx then why weren't they there sooner? I mean we waited until the next day to go there. But instead of going to the Citadel the minute Alliance command knew about it those mercs appeared only hours before we did."
"Yeah well I thought it was just luck we got there in time."
"Something else is wrong Kaidan whenever we get a lead on them, they disappear before we can do anything. Now the attack on the council? Think about it for a minute, it just so happens to take place at the same time Admiral Hacket has a meeting with the council."
"Coincidence?"
"Maybe but it's starting to be a few to many coincidences to my liking."
"Keep searching and Liara maybe we should keep a close eye on our councilors and the Admiral for now. Maybe we find a leak somewhere."
Liara nodded and fiddled with her data pads. Kaidan knew she would be reassigning the brokers contacts in the next few days. Well the more Intel she could provide, the better their chances became of catching these bastards.
Kaidan left Liara to her work. It was getting early anyway, soon everyone would be busy doing their daily tasks. Kaidan wanted to be alone for now. His thoughts wandering of to Shepard regret filled him, regret he didn't have a chance to truly spent time with him. Regret that he never would never have a chance to tell him how he truly felt. He knew Shepard was gone, the only mystery was how and why anyone would want to hide his body.
Kaidan sat alone in the med bay, his dreams haunting him. "You know I'm gone Kaidan. Just think, you already know that." Johns voice repeated in Kaidan's head. He knew there was no way John would have survived Kaidan just didn't want to admit it. But he knew.
"You Failed us!"
"Yeah know what? Screw you. You're stupid mercenaries suck." The pain overtook his body, no he couldn't give in he has to resist it.
"We can force you to do as we command." The voice got angry.
"See I get it now you can't actually force me. Sure you can torture me, you can control me to a certain degree. But what did that Asari scientist say. 'There is a balance between control and usefulness', sure you can try to completely control me. But what good would I be as a mindless hull to you." He grinned, torture was bad yes but he was sure they needed him for something.
"You feel smart don't you? But this isn't some reaper indoctrination. We have other methods to control you." The voice was getting angry.
He braced himself, any moment now they would make him regret speaking up, but it was worth it he knew he had hit a nerve.
"You know screw you, maybe you can force me to do your dirty work, but you will regret it!"
The response didn't take long, a flash of pain forced him on the floor.
The pain took over his whole body until he passed out.