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.

Answers

Kaidan was somewhere nice and warm. Something felt good here, he couldn't see anything but everything was light around him. The light gave him a feeling of comfort, of inner peace.

"Kaidan?"

A whisper, it called him he turned to search for the source of it.

"Kaidan? I'm sorry."

"Shepard? Is that you?"

"Yes Kaidan I'm here, part of me is anyway."

"What's here? Where are we?"

"I don't know Kaidan I've been here a while it's just here i guess."

"Shepard you're not making sense what is here where are we?"

"I can't explain it Kaidan. I'm here sometimes i can be somewhere else, but it's getting harder to not be here."

"So you're alive then?"

"Maybe i can't say anymore. Kaidan I'm sorry I should have..."

"Wait! Shepard, I need to tell you..."

Kaidans eyes suddenly opened. He was disoriented What happened? His shoulder hurt and every muscle in his body ached. He tried sitting up but everything hurt so badly he fell back in to his bed.

"Glad to see you're awake. Had us all scared there for a moment."

"Chakwas?" He couldn't see anyone.

"Yes Kaidan, I admit didn't think you wake up so soon. That was a close one. Thought we lost you there for a second."

"How bad is it?"

"Clean shot, ripped right through your shoulder. A concussion and your vitals where dropped almost as if something drained the life out of you."

"What about the others, what happened to the opposition we faced?"

"The others are okay and why don't you ask them yourself, Garrus has been bothering me to see if you where alright all day."

"Thanks doc."

"I'll sent Garrus in."

Half an hour later Garrus came in with a tray of food.
"Hey Kaidan, got us scarred there for a minute. Also the doctor said to force this levo crap on you."

"Some leader I am, first time out and I nearly get everyone killed. So what happened after I hit my skull?"

"After you went down the strangest thing happened. The leader of that group suddenly ran away leaving his men behind. Bailey and the Aria's mercs could finally use the distraction and attack from behind. Got everyone except for the leader."

"ehm, Garrus did you hear his voice?"

"Not really, why do you ask Kaidan?"

"Nothing just before i got hit... I could have sworn it was Shepard."

"Kaidan you might have hit your head harder then we thought."

"Yeah must have been the concussion or the blood loss."

Kaidan played with the food on his tray. "Heck I should probably just sleep it of for now."

"Just tell us if you need anything. But resting until you're better would be a good idea. Liara is already gathering information in that area Bailey secured. Aria even threw in a dozen more mercs after she heard that someone had attacked Bailey's team. Something about it being personal now."

"Yeah, she seems to like Bailey. You don't think..."

"Kaiden, I wouldn't dare think about it. But it really looks like it." Garrus pointed at Kaidans food. "Now eat and rest, we will do the rest and tomorrow we might know more."

When Garrus had left him Kaidan closed his eyes. His thoughts haunted him, was it really Shepard maybe he was just hallucinating. Might be his mind was just playing tricks on him. He had been thinking about Shepard the whole day, what if it was all just in his head? But then again what if it wasn't.

"Deimos care to explain why you didn't complete the mission?"

"Yeah about that... Something important came up."

"We don't care about excuses. You will do as you are told."

"You know I don't care what you want, stop forcing me to do your dirty jobs." Pain soured through his head. It forced him to his knees.

"We made it clear before, you do as we say or we will make you regret it."

"Screw you, I will..." Again that searing pain, he knew he couldn't resist for long anymore.

"You will do nothing, you will do as we say. Now we want you to go to the following coordinates and retrieve something for us. Don't fail us again or you will regret it."

"Shit... You... one day..." He lost control, his body acted on it's own again.

The next morning Kaidan felt a lot better. Chakwas had given him some great pain meds and it had been a nice dreamless sleep. She had make him promise to keep it easy for a few days but had agreed to let him go as long as he kept out of trouble. Though he had to admit the woman had learned a lot in the last few years, she had even tapped his arm tight just to make sure he wouldn't use it. He was pretty sure something in those meds she had given suppressed his Biotics

While he was trying to balance his food tray on one hand, while making his way to the table. Garrus suddenly grabbed his tray.

"Kaidan you could ask for help you know."

"Garrus, I believe that crafty old woman drugged me! Can't believe she suppressed my Biotics."

"No Kaidan, Liara gave her those pills. Just making sure you weren't going to kill yourself doing something stupid. The doctor said you where already exhausted."

"Damn everyone is conspiring against me now?"

"How do you think we got Shepard to hold still whenever he landed in the medbay?"

"Damn so it's a conspiracy against Biotics? I'm really screwed now." Kaidan felt regret, Shepard he missed him and here he was making lame Jokes.

Garrus must have seen the sadness in Kaidans eyes.

"Hey eh, Kaidan you're up to do some work today?"

"Like what Garrus? Chakwas told me to keep out of combat."

"Yeah no Chakwas would kill me if I gave you a gun... That woman has all kinds of scalpels and pointy things, she could be dangerous."

"You're afraid of needles Garrus?" Kaidan had to laugh.

"No just afraid of doctors who like cutting in to living beings.
Anyway Liara has analyzed the evidence from the citadel. She and James are returning with Andersons body as we speak. We want to put some holo projectors in the shuttle bay and try to reconstruct what happened there."

"She found anything useful?"

"She said we wouldn't believe it."

"Okay, just call me wen we are ready. I need to do something first."

"Sure will Kaidan. I need to calibrate Liaras projectors anyway."

After Kaidan had eaten he went upstairs he still hadn't read that message Shepard had left. Now he needed to know what was in it or he would never find any peace of mind.

Kaidan,
If you are reading this then I must have died.
I Hope we defeated the Reapers before you ever see this, but maybe that's too much to hope for.
Anyway Kaidan I needed you to know I'm sorry.
Sorry for not telling you that I love you.
Sorry for not explaining why I turned you down.

But I need you to know why I couldn't allow it. Back when I was a young stupid marine, I had fallen in love with another Soldier, Dean. Even though it was against the rules we just didn't care. When we planned our shore leave together on Elysium.

Well you know how that turned out.

But what most don't know is: Dean was there with me. Kaidan he forced me to keep everyone safe, but Dean he didn't make it out. Dean had gone behind the enemy lines to lure them away from us. I saw how he got shot. I had wanted to go to with him, but he had made me swear to keep everyone safe. He was the real hero.

After that I just couldn't get involved with someone again, the pain of losing him, I didn't want to go through that again.
But after Virmire, I always asked myself if I chose you because it was the right thing to do or because I was in love. I couldn't let my feelings cloud my judgment so I pushed you away when you laid out your heart before me.
I was afraid Kaidan, Afraid to lose you, afraid to make the wrong choice so I tried to run.
Please forgive me.

John

Kaidan looked at the time-stamp. The message was written at the night before they attacked the Cerberus base. Kaidan couldn't hold back the tears anymore. "Shepard why didn't you tell me, I would have understood." Kaidan whispered to himself.

Kaidan just sat there for a while thinking about all the lost chances, the time they could have had together. At some point Garrus had signaled for him that they where waiting for him in the shuttle bay.

It had taken a while but Kaidan had gathered himself again. Splashed some water in his face and got to the Shuttle bay.

"Before we start, I have just spoken to Tali. She managed to sneak in our little bugs and we should be able to have full access to Alliance and council databases soon. Also my own sources are slowly back online and there are some interesting reports about those mercenaries you encountered yesterday." Liara said while flipping through pages on a data pad.

"So we know who sent them?" Kaidan asked.

"No, we only know that since the end of the war a new group of mercenaries has formed. They are heavily recruiting from among the Refugee camps. The group is called Styx. Otherwise not much is known at this point."

"Wait Styx, why does that remind me of something?" James interrupted her.

"Because it's ancient Greek it means something along the lines of hate or detestation" Cortez said.

Liara looked at her data pad again punching in some new data. "I'll look in to possible meanings of the name. But I think we should go through the reconstruction."

Edi turned of the lights and the projectors painted a large room at the end of a hallway.

"This here is the continuation of the same hallway you guys where in yesterday. Now some things are unclear but by using blood and DNA traces these are the bits we can put together... Well see for yourself." Liara explained.

The Image showed Shepard walking towards the large room. Stopping a bit before a console where a man stood.
The Image of Admiral Anderson appeared on the hologram.

"So we know that Anderson stood over there and Shepard came in from here. But then we can't say for sure what happened."

Liara hit a button and the holo changed. "Now from the Ballistics and the blood we found we reconstructed the following..."

The holo Shepard fired a single shot and Anderson was hit in the abdomen.

"Wait what the commander shot Anderson? That can't be true." Steve said in disbelief.

Liara shook her head. "It sure seems like it. The gun, the ammunition. The amount of blood on the floor suggested they stood there for a while before the shot was fired and the gun and ammunition well maybe a handful of people would have had those. But there is more. Something even stranger happened."

The image of Shepard walked to the console and went back to Anderson. Shepard and Anderson sat next to each other.

"So after Shepard shot Anderson they sat next to each other?" Kaidan asked.

"Yes the body of Anderson was found there while a blood pattern from Shepard is towards him massing next to him and then at a certain point back towards the console. Also we know that Admiral Hacket spoke to him at some point. Shepard said he didn't know how to... and he couldn't see. Which suggests he tried to activate the crucible from here."

"So whoever attacked us didn't want to know that Shepard was here or what?" Kaidan still didn't understand what was going on.

"No it's even more strange then that see this floor plate right in front of the console? Well there isn't one there also no blood from anyone. As if it's missing."

"Okay Liara anything else?" Kaidan was confused why would Shepard shoot Anderson it didn't make sense.

"Yes in fact. The ring was found a few stories below this room, also there was a lot of Shepards blood between a pile of Debris near the ring. Actually it looks like that pile of debris fell down from somewhere above this room.
Also the so called body of Shepard was in a completely different part of the citadel no way he could have gotten there on his own. " Liara took a deep breath and looked in the faces of the others.
"At some point there must have been a third person in this room we found a bit of blood splattered near the edge. But since there is a large part of the floor missing where everything fell down. We can't be sure if it's even related. We would need to identify what parts of the rubble fit to that floor to find anymore traces of whoever was up there."

"Damn, the third person anything we could use to find out who it was?" Kaidan hopped that would give them an answer.

"No records what so ever, as if he was scrubbed clean from all databases. But we know it was a Human Male and he was a smoker."

"Okay we tell the council the mission was a failure. I want this thing kept secret until we find out who those mercs are and what they want."