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.
Citadel
"Citadel this is Steve Cortez from the Normandy shuttle. I have a spectre on board, requesting permission to dock."
"Citadel to Normandy shuttle spectre identification is required."
"The spectre is Kaidan Alenko, he is sending identification codes now."
"Normandy shuttle, your cleared for docking. Aria want's to see him in Purgatory immediately."
"Well, at least they didn't shoot us out of the sky." Steve turned to Kaidan.
"Somehow I think something big must be going on here. Did you see the defense turrets pointing at us?" Kaidan had a bad feeling.
"Don't worry Kaidan. Aria want's to see you for some reason. While she may be a though one. She always does what she thinks is right, even if her methods might be a bit extreme." Garrus thoughtfully assessed the situation.
"You're sure about that Garrus?" Kaidan really wasn't that sure, what if it was a trap.
But no time to second guess anymore, the shuttle had docked. At least they would find out soon what Aria knew or what game she was playing.
When they stepped out of the shuttle a Batarian greeted them. "Aria want to see you, don't keep her waiting."
"Hey aren't you the guy from the bar on Omega." James interrupted.
"Aren't you the guy who tore a vid screen from the wall?" The Batarian simply stated.
"Dioz mio, the universe is small. Sorry about that back then."
"We should move, Aria hates waiting." The Batarian glared at James.
"Anything we should know about James?" Kaidan whispered.
"Nothing to bad, just a disagreement with some Batarians on Omega back when Shepard blew up the Alpha relay."
"Aria is inside. Please refer from killing, shooting or destroying anything inside." The Batarian rubbed his knuckles while he nodded to the door.
"Okay guys let me do the talking just keep on the lookout for trouble." Kaidan said and went inside.
The place was as if not a single reaper had ever touched it. The music was deafening, people where having a good time, there were even some Asari dancers on the elevator platforms. On the left side of the stairs 2 Batarians blocked the path.
One of the Batarians stepped infront of Kaidan and scanned him.
"You know, no need for scanning we have our weapons right here."
"Just making sure you are really the spectre we are awaiting. Don't you guys ever expect anyone to confirm you're identity? All clear let them through." The Batarian moved to the side.
"Kaidan Alenko, before you ask. Anyone could claim to be you. My people are just making sure you are who you claim to be. Seems you have that ignorance from Shepard or is it a human thing?" The Asari said mockingly.
"Aria T'loak i presume." Kaidan looked at the Asari, Deep blue, a bit of an attitude. She barely recognized his presence there. She was everything he had heard about her.
She slowly clapped her hands. "Congratulations, you're not as stupid as I thought you would be. You even brought Archangel, you might be a bit smarter then you let on Alenko."
"So enlighten me Aria why did you require a Spectre to retrieve a body?" Kaidan got impatient, this woman was toying with him and he didn't like it at all.
"Someone tried to use me, NO ONE does that unpunished. So the only logical conclusion was to ask for a spectre the moment it was clear you where back."
"Sorry Aria but I don't get it, why do you need me for you're personal problems again?"
"Since they used me in some cover up. I assume the thief went to you instead of to the council. It is what I would have preferred if I had known you where coming back."
"She did." Kaidans hand went automatically to his hearth where the ring was under his armor.
"From your reaction I can see you have it then. It was found somewhere completely unrelated to the body. So tell me why would he part with it?"
"He wouldn't, the place he kept it was secure enough that he wouldn't loose it by accident."
"I thought as much, also that same thief who i saw in Shepards company back on Omega warned me of something.
There are certain elements on this station that are plotting something, covering up evidence and killing those who know about it. Still sounds like a basic body retrieval?"
Kaidan had to admit it wasn't an easy task anymore and Garrus was right the woman might be a bitch but she was at least honest about why she wanted him.
"No, not really."
"Now tell me something Alenko. How many reapers used modified spectre grade weapons and special ammunition?"
"What? ehm... none I would say, but what does that have to do with it?" Kaidan was confused now, she was playing him.
"Then why do i have the corpse of a fucking Alliance Admiral, with a bullet in it that could only be fired from a M-77 Paladin using Warp ammunition?" Aria was angry blue biotic energy flowed over her body.
"You wait.. WHAT? It can't be!. That would mean..."
"Yes Alenko now you know why i wanted a spectre, actually why I wanted you, something is wrong. Even more so since Commander Bailey and a group of my men wanted to secure the area till you arrived. We lost contact 5 hours ago. So I ask you who is fucking with me?" Aria got really angry, if her eyes could kill someone would have dropped death in the vicinity.
"Damn this is, just not right. Aria Where do we need to go? Garrus, James prepare for combat we don't know what happened."
"Well at least you are quick to take action. I'll give you the coordinates and a route. Oh and Alenko I would appreciate it if you got Bailey back to me. He is kind of useful to have around." Aria had an insisting look in her eyes.
"We will do what we can, I promise."
Kaidan checked his gun two times before they even left purgatory. Bailey not reporting in after securing the area can't mean anything good.
"Hey eh Kaidan, what was that about the gun?" James asked pulling Kaidan from his own thoughts.
"See my pistol? Shepard bought it, Spectre requisitions, it costs more then half our armory. The ammo Aria talked about? Well I know three people that know how to do that. That crazy biotic Jack we met at the party, Liara and she thought it to Shepard."
"So we are looking at someone who has access to spectre guns and a biotic trick, who was accidently on the citadel during the attack... You don't assume he.." Garrus couldn't finish his words.
"I don't assume anything, who knows what happened no need to speculate. But the ring, Aria stating that it was somewhere else as his corpse. It's just all to much to believe in coincidence." Kaidan sure hoped that it wasn't what it looked like at the moment. If Shepard had killed Anderson... Now that would make things complicated.
They ran from hallway to hallway following the path Aria had given them until after a while they arrived in a dark, bad smelling corridor.
"Is that blood?" James knew the answer before he asked.
"Reminds me of the collector base." A cold shiver ran over Garrus' back.
"Intruders, stop them at all costs!" They heard from somewhere in front of them.
"Bailey? That you?" Kaidan yelled.
The response was instantly, bullets flying in their direction.
"Guess not Bailey." James said while he loaded his gun. "Let's rock this shit!"
Garrus took cover behind a large pile of bloody remains. Sniping anything that popped up for a second. James drew the enemy out by running in the middle and presenting himself as a target whenever his shields where full. Kaidan waited for the right opportunity freezing enemies so Garrus had a clear shot or overloading shields so the others could take the enemy out.
They had to fight for every meter to advance through the corridor. Until at some point they could hear someone yell commands to their enemy.
"Take out their Sniper you morons. Who the fuck thought you guys to fight?"
"Forget the meathead don't you see they have a Biotic, damn everything I have to do myself."
Kaidan couldn't believe his ears that voice...
"She..." He had barely spoken when he felt as something ripping him apart. He was weakened, something drew the life right out him. Then his shoulder was hit, a bullet shred right through his armor, Kaidan dropped his gun. Before he could pick it up again, a white flash hit him and he was thrown into the wall then he lost consciousness.