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.

Debriefing

The debriefing went rather smooth. Hacket had been suspicious at first but he council had backed their claims about what happened on the citadel.
Kaidan suspected that Liara's Intel might have been enough of a tip for the council.

Preliminary reports about the Destiny Ascension where more interesting. Someone had tampered with the security systems, giving Styx complete access to the whole ship before attacking.

"So let me get this straight Admiral Tali'zorah had a way of contacting you all along?" Hacket said disapproving.

"Yes, well we left her communication codes intact wen we went dark." Hers and a few dozen of the brokers Kaidan thought.

"Okay I get why you went dark after that encounter on the citadel. But why not give a report to the council or me?"

"Admiral we couldn't risk that a leak near either the council or alliance command tipped of those mercenaries."

"Okay any theories why did they went after the council then?" The Admiral wasn't happy with what little answers he was getting, but it's no use to argue with the councilors anyway. They made it pretty clear that their Spectres had a free hand in the matter.

"We suspect the council was only a secondary target. The one giving orders was actually near the labs. Sir, from what we could reconstruct it seems they where after the Geth."

"Why the Geth? What would a mercenary group want with the Geth?" Zaal'koris asked.

"We're not sure but since they used a EMP-explosive it was probably get the data or destroy it. The only thing that bothers me is that they waited days after the Citadel attack until the day Tali activated Charles." Kaidan pondered. "If they wanted the data or just destroy it why wait until a Geth is activated?"

"Oh Major, just one thing. Your report states the leader knocked you out before the explosion. Why didn't he just kill you?" Hacket inquired.

"I have been asking that myself. It could be he thought the explosion would take care of it." Kaidan was grasping for an explanation.

Hacket thought a bit about what was said before addressing the council. "Councilors, since the destiny ascension is compromised, I would suggest to relocate you to one of the Alliance ships."

"No need Admiral, we decided to stay with the Turian fleet. Their ships seem a lot safer for now, outsiders would stand out more within their military." Aethya grinned. "Hell we would be the only aliens on their ships, unless these mercenaries can find a bunch of Turians to infiltrate the ship, we are safe there."

Kaidan nodded, "Admiral we have arranged transportation for you to return to the Alliance. I will personally see to it that the council reaches their new destination after that."

He awoke on a cold metal table, bright lights shinning in his eyes. His eyes adapted to the bright light, he slowly got a better image of his surroundings. Some kind of medical facility, monitoring devices everywhere. Who ever had put him here the straps around his hands and feet suggested that the someone was not friendly.

He could hear someone talking in the distance the sounds where muffled but he could pick up on some bits.

"Sir we don't understand how he could resist in the first place."

"I don't care, I want him under control. Brainwash him, remove his memory. I don't care how you do it just go it."

"Sir, just if we go any further Deimos could become a total loss."

Shit they where talking about him, what the hell where they doing to him.

"Damn he is awake, put him under."

He struggled, but it was no use he couldn't get free. The drugs where pulling him under, just before he was gone he remembered.

The Admiral had left the Normandy, one of the few things Kaidan was actually happy about. The council would stay for a while longer, at least till after the funeral. That was one of the things Kaidan really didn't like. The council has opted to fast track Shepards funeral, so now everyone had to go to a ceremony where they would put a fake body in a casket.

Even if it wasn't Shepard Kaidan didn't like it one bit, he couldn't shake the feeling that everyone was to eager to give up on Shepard. Okay, he admitted to himself except for the Normandy crew no one really knew that it wasn't Shepard but still.
Kaidan decided it was probably a good idea to let of some of his frustration, a bit of training in the shuttle bay seemed like a good idea.

The second the elevator doors opened he heard cheering. Hannah had just turned around and held her arms up in victory. "See, MR. Vega that is how you throw a strike, now drink."

"The hell is going on here?" Everyone turned to Kaidan.

"Mr. Vega here said he would go easy on me if we played a game." Hannah grinned.

"The stupid pyjak even agreed to take a shot whenever she throws a strike." Wrex roared and hit James on the shoulder.

James took the shot glass and downed it quickly. "Damn, the whole family is mean wen it comes to games."

"Mr. Vega, we only play to win. A quick search could have told you that I have a perfect game every once in a while." Hannah threw the next strike and looked with a slightly evil grin to James.

"Shit... Never bet against a Shepard." James drank another shot.

Kaidan needed to get out of here, even his friends and family had given up on Shepard.
He spun on his heals and left the shuttle bay.

Two days, two days had passed and the enemy hadn't shown their face.

Damn this was depressing, the waiting was too much to bare. Kaidan sat in total darkness on Shepard's bed.

They hadn't achieved anything in the last two days. Not a single new lead had opened up and Tali was still working on Charles. Maybe the Geth could help them out, maybe he would remember something about the Mercenaries. It was as if the Mercenaries had just disappeared out of the system.

Tomorrow they would have to go to the Funeral, he almost hoped that Styx would come and crash the party. Would be more interesting then sitting through a funeral for a clone anyway.

Kaidan lay on his back looking out the ceiling window. The view was spectacular, he had a straight view at the asteroids near Jupiter. Kaidan had to laugh Cerberus, Styx all Greek mythology and they had chosen to hide the council among the Trojans. Next thing we know the Greek war gods themselves would get involved in this.

Kaidan crossed his arms behind his head, and whispered to himself.
"I'll find out what they're up to John, I owe you that much."