Spoilers: obviously content from the games including the Ending.

For the most part this will follow ME lore, just adding and adapting.

Illusive

Kaidan felt the tension leave his body. He turned to look over the base, a few dozen heavily armed Turians where locking up the remaining controlled alliance personal. There was a first aid station in the main hall where they where patching up the Alliance personal.

Kaidan noticed the young Turian talking to some others. Only now did Kaidan notice that he was basically still a kid maybe 16 or 17. He walked over towards the Kid. "Hey, I wanted to say thank you for helping my friend out there. Didn't catch your name."

The Kid saluted. "Ahern Asclepius, Sir it's an honor to be of assistance."

Kaidan offered his hand. "Stop saluting. I owe you one."

The kid looked a bit overwhelmed, not knowing how to react. An older Turian next to him cleared his throat. "You're supposed to shake his hand, it's a human thing." The kid immediately grabbed kaidan's hand shaking it wildly.

"Sorry Major, he's still young but a great field medic. excuse me, I should introduce myself, General Vicarious of the ninth platoon" The older Turian stepped forward. "But tell me is it true, the man he helped is it really Commander Shepard?"

Kaidan knew there was no use in hiding it anymore. "Yes, the one and only. Though not even the Alliance knows he's alive."

The young Turians face lit up like a Christmas tree. "Think I could get an autograph once he's healed."
The general shot a serious look towards the kid.

Kaidan had to smile at the thought, John signing autographs he would probably rather flee across the galaxy. "Crap he'll probably hate me for it but I'll ask him."

The kid saluted and left to tend to his patients.
"Didn't think one so young would be here in the field, tending to humans no less." Kaidan watched after the young Turian as he gave orders to his comrades.

"The war has left us with little options, our youngest recruits were sent to the field. He's one of those who learned the hardships of battle in the field and grew from the experience. Has a knack for xeno-biology too." The General seemed proud of the young medic.

"Anyway General what is our status?" kaidan had to keep busy, trying to find meaningful things to do. His only other option was to pace nervously before the room they had shoved Shepard in.

"My troops are rounding up the last remaining Alliance soldiers. We're patching up the wounded, some of the non-hostile soldiers were locked up in the barracks. For now we're keeping them there. At least until this situation is cleared up with Alliance command." The General flipped through his data pad. "Also, the council can't stall the alliance for ever. It might be a good idea if a certain spectre tells them we took over their base on his request." The General threw a knowing look towards Kaidan.

"Yeah right, I imagine Admiral Hackett is about to explode at the moment. General if you could follow me to the Normandy we should probably talk to the council and Alliance command." Kaidan could just imagine how some voices in Alliance command would be speaking of invasions ad demanding retribution. Most of them probably loyal Styx followers too.

"I know how it might seem Admiral, but we assure you there are good reasons for all of this." Hannah hoped they would soon get any news from the Normandy because Admiral Hackett was starting to get to her.

"With all due respect councilor, this is getting ridiculous. I want to now why we aren't allowed to retake our own base from a Turian invasion fleet. Hell, give me one good reason why we shouldn't kick them out of the solar system after such a grave breach of the peace treaties." Hackett was getting angry.

"No with all due respect sir, but the Turians acted upon the councils request. We didn't see any other way to solve our crisis." Hannah shot a quick look over towards the other councilors in the corner of the room. Victus only shrugged his shoulders. Enough for her to know they hadn't yet reached the ground forces they sent.

"This is outrageous on what basis would the council even have the right to occupy on of our military facilities." Hackett's face was turning red.

"On the basis of Treason, we lost two spectres and half a ship's crew investigating that place." Hannah lost her cool that moment. A large hand rested on her shoulder, Wrex was standing beside her.

"Admiral, just be happy I didn't send the Krogan to clean up." Wrex smirked knowing too well the Admiral would have something to think about for a moment.

"Damn, I hope you know what you're doing. Command is getting restless, there are those that won't let this one go easily." Hackett calmed himself.

A light blinked up signaling an incoming transmission. "Normandy is reporting in, Major Alenko and General Vicarious want to speak to the council." A voice over the intercom said.

"Put them through, Admiral you might want to hear this." Hannah sat down in front of the table.
"Spectre Alenko, just so you know we are patching in Admiral Hackett for this. In case there is anything concerning classified information." Hannah folded her hands together in front of her.

"Understood councilor, first of General Vicarious' troops have gained control over the Rio base. All Alliance personal is under house arrest until we can clear them."

"Alenko you knew of this?" Hackett's voice sounded of disbelief. "And what's this about house arrest?"

"To be clear Admiral I didn't really know much about the situation, until I was being kept prisoner by an Alliance officer working for Styx or should I just say he was Cerberus all along. The other spectre set of a distress beacon before launching a suicide mission to disrupt their plans." Kaidan was trying to keep it short, Hackett could read everything in the reports he would have to write anyway.

"You mean he? Is he alright?" Hannah had a hard time keeping herself leveled.

"The spectre in question is in surgery right now. Since we also found Miss Lawson being kept hostage on the base, I'm sure she can patch everything together again."

"So you're telling me Styx had taken over an entire Alliance base and nobody knew they where keeping hostages? That's hard to believe." Hackett shook his head not wanting to believe his ears.

"Admiral It's exactly as it sounds. The Alliance isn't only compromised, they're turning our own people against us, implanting them with control chips. We can't say how many of the higher-ups are either under control or doing this of their own free will."

"But that would mean..."

"Yes, anyone could be our enemy. Admiral I think it's time we set up a meeting We have to tackle this problem at the roots and we will need all the help we can get."

"Alenko I hope you know what you're doing. If it's really this bad then..." Hackett had grown pale over time.

"I'll set something up as soon as our spectre is back on his feet. But Admiral Hackett I must insist we keep the Turians in charge of Rio for now."

"Damn, Alenko I don't know how Alliance command is going to take this." Hackett shook his head, this could as well become the death sentence for his career.

"Just tell them that Rio was infiltrated by an unknown enemy. Watch their reactions. Maybe we can find out if one of them is on Styx side in all of this." Hannah interrupted the two of them.

"Okay, I better not regret this."

"You won't sir." With those words being said the connection was cut off.

The man exhaled slowly, smoke filling the air around him. He only ever spoke of how he did everything for Humanity. It made John sick, the Illusive man always went to far. He had another name on the tip of his tongue, he tried concentrating on the smoking man, remembering the thick blue smoke in the air. The voice, then it came to him he had seen him somewhere else. The man with the strange black spots on his face. The one who shot the Admiral. The one who had shot himself.

"Phobos"

The man with the blue scaring, the one with the blue glowing eyes. The one who had manipulated him into attacking the Normandy's crew. The one who had always whispered n the back of his head. The voice that controled him.

John's body janked upwards, eyes wde open. "I know how to find him."

John felt a tense grip around his hand suddenly relaxing. "Find who?" A sleepy voice said next to him.

"Phobos, The Illusive Man. Whatever he calls himself now." John felt a hand push him back down.

"Whatever it is it will have to wait Commander, for now you should rest. I can't keep bringing you back from the death." Miranda applied a bit more force to make her point clear.

John let himself relax against the pillow. "Say kaidan, shouldn't you be on the Normandy?"

"And let you gain all the glory again? Don't worry the Normandy is parked nearby. Besides someone had to save you're sweet ass this time." Kaidan grinned as he heard Miranda make a short snorting sound.

"So how bad is the damage? Everything important still in place?" John threw a short glance towards Miranda. "Or did she take a souvenir."

"No Commander, Everything still where it belongs. Though you'll need to rest for a few days. But the damage itself should heal up quickly. For now you should really just sleep and let your body recover for once."

John nodded, he needed some time to come up with a plan anyway.

John had spent the whole morning talking with EDI and Charles. The plan was slowly manifesting itself.

"So I think they really wanted the Geth in order to use them for a more solid network in controlling their people. Since that failed when Charles escaped they must have been using short-range transmissions whenever possible."

"Possible, the Geth networking capabilities would have given them the means to even control people across relays. Failing to get them we can assume they have been looking in to other plans. The Illusive man always had a backup plan." EDi was studying the control chip schematics Miranda had given them.

"So? Is it possible? Can we really locate them by using the chips against them?"

"Yes, but aside from the risk you would have to take we also require a transmitter strong enough to cover the whole solar system."

"Yeah I know the risk believe me I have no intent on becoming one of their drooling followers again. For a transmitter well how about the Citadel? If we can make a big doom device that destroys all synthetic life in the galaxy then it can't be too hard to use it as a signal booster."

"It could work, but still it's a big risk."

"I know that's why we need to keep this quiet for now. We only want to infiltrate their facilities and gather as much information as we can ." John looked over the elaborate plans the AI's had composed while they had talked. If they where lucky for once this might just work.

John had sat in the cargo bay of the Normandy for a while now seeing how James and a few other crew members where playing one bowling game after the other. For now he couldn't really do much but wait, Kaidan was making the last arrangements before they would start moving Miranda's patients towards the Citadel. Those marines on base who hadn't been controlled would stay behind together with the Turians.

But until they actually reach the Citadel he wouldn't be able to do much, so the only thng he could do was sit there and wait. Well wait and think about his strange memories that where trying to resurface.

"You look like something the cat dragged in." An obviously tired Kaidan sank to the floor next to John.
John got pulled away from his thoughts. "Looked in a mirror recently?" But he regretted immediately saying it when he saw how tired Kaidan was. "migraines?"

"No just tired, everyone wants something from me right now. I just want a moment for myself." Kaidan leaned back closing his eyes.

"So when are we going towards the Citadel?" Johns hand stroked through Kaidan's hair.

"Tonight, Aria has seen to it that we have a large part to keep all those unfortunate enough to have become Styx pawns. Plus Miranda can have access to the medical facilities on the citadel, at least those that are still in a working condition."

"Hmm... So it seems you have some time off should we go to my cabin or your's major?" John had a wicket smile darting around his lips.

"I have a cabin on this ship?" Kaidan raised an eyebrow.

"No, but I can offer you a closet for your things in my room."