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.
Doubt
"How is Project Deimos coming along?"
"We should have results within the next 24 hours, the preliminary tests are positive. The implants should all work within the set parameters."
"Good, Report wen Deimos is ready to go."
Two days after their return to earth.
kaidan had awoken that morning feeling much better. There was at least a small hope that the corpse wasn't Shepard after all. Just now the question remained how to tackle this new problem. He couldn't tell just anyone. kaidan walked to the mess to grab breakfast while he considered who to talk to wen suddenly he bumped in to an unexpected face.
"EDI?"
"Yes, kaidan. Sorry I was just on my way to see Jeff."
"Wait you're back? Weren't you ehm... gone?"
"I suffered some kind of disablement. But Tali was able to replace the broken routines with my backup. I have some kind of ehm... Let's call it memory loss though. I have nothing in my databases after the attack on Cerberus. But Tali assured me we have defeated the reapers."
"Oh yeah they mentioned a backup, just didn't expect to see you so soon i guess."
"kaidan? Can i ask something?"
"You just did EDI."
"Oh I see my inquiry to ask a question was a question by itself. I shall adjust my programming to avoid such problems in the future."
"Ehm, okay you at least didn't change much. So what did you wanted to ask?"
"kaidan while the crew seems under a certain level of stress and despair due to the loss of Shepard your vitals are strangely relaxed. Why is that?"
Well no hiding the truth to an all knowing AI, well there he had someone who could help him at least.
"Well EDI, you might be the one to help me with a... ehm problem. Actually you might be the best choice to see if what I think is possible."
"Okay Major, we will talk in a moment i want to see Jeff first if that's okay?"
"EDI go and see him. He sure can use some good news for once."
kaidan went and grabbed his breakfast. At least some things can be fixed by a software update.
After an hour he met up with EDI in the AI core. She didn't have full control over the Normandy's systems yet so he had to wait for her platform to arrive.
"Edi by now you heard everything about Shepard I presume?"
"Yes, his death is the first thing everyone speaks about."
"Okay what if i told you I believe he isn't that corpse they found?"
EDI stayed silent for a moment. "kaidan I just went through the Alliance reports, they are accurate."
"Yeah, everyone tells me that but... Do you remember the Party on the Citadel?"
"Of course I remember."
"Do you remember this?" He handed her the ring.
Edi turned the ring. "This is the ring I gave to Shepard, he carried it on his dog tags. What is this about kaidan?"
"EDI that ring was not on the corpse they claim was Shepard. It was even found at a different location on the citadel."
"Is the source reliable?"
"Kasumi gave it to me two days ago. She was hired to deliver it to Shepards mother."
EDI paused for a moment. "Then kaidan the other possibility is... The corpse is a clone and someone did not know about the ring. Normally it would be to improbable to suggest. Then again Shepard is known to have had at least one clone and do the implausible."
"EDI, see that's why I really love that you're back. You don't just believe me with little convincing. You just solved my last question."
"kaidan, I would caution you not to tell everyone. Whoever placed a false body for the Alliance to find could have a high level access."
"I know EDI. But in order to find out what happened to him we will need some help and a plan."
"I would suggest keeping this to the Normandy's primary staff."
"Yeah, we will need to talk to them. EDI lock our conversation down, use my Spectre authorization and make anything involving our last conversation restricted."
"I would advice you to hide the ring kaidan."
"Yeah, i know just the place to keep it EDI." kaidan took his dog tags and hung the ring on the chain. Hiding it under his clothing.
"Admiral Hacket, sir." A young Marine ran up to him.
"What's wrong boy?"
"Sir, Commander Bailey just reported in. The teams on the Citadel have found the body of Admiral Anderson."
"Good to hear sent an alliance team to recover him."
"Sir, there is a slight problem. Aria refused to let any alliance military in the vicinity of the body."
"What is this all about all of a sudden?"
"Sir Aria specifically said to sent in spectre or she would personally kick our men out. She might have used some different words though."
"She better has a damn good reason to act up all of a sudden. I'll take care of it."
"kaidan priority message from the council. Just let me know if you want to pull a Shepard on them EDI improved the lost signal routine." Joker's voice sounded over the com system.
"Joker not cool, I would never do that."
"Yeah that's what you say now but just wait until they start ignoring you too."
"Joker, quit it. I'll take the call in the Observation lounge."
kaidan locked the door so no one would disturb him. Then he activated the vid-conference.
"Councilors? Anything i can help you with?"
"Hey kaidan got a job for you. Hacket 'requested' to send someone to meet with Aria T'loak. It's kind of simple he said, go to the citadel grab the body of Admiral Anderson and return it to the Alliance." Wrex grinned while he explained the task.
"Ehm Wrex you're kidding right? Just a pickup? Why would you need me for that?"
"Well there might have been a mention of Aria threatening to tear the Alliance soldiers a new one. So he asked us to sent a spectre." Wrex almost laughed wen he said that.
kaidan considered a moment telling the council his suspicions about Shepard. But decided against it and hey he was being sent to the exact person he wanted to see anyway.
"We will go as soon as I have my crew ready."
After wrex cut the connection kaidan started walking back and forth. "Aria stopping the alliance to get Andersons body is strange. Sending Kasumi with the ring is even stranger what is that woman up to? But the big question is what does it have to do with Shepard." He murmerd to himself.
After a moment of collecting his thoughts he decided he needed his team to figure it out.
"EDI, I want the main crew assembled in the observation lounge."
After everyone had arrived he locked the door again. "First things first whatever we speak of can't leave this room." Wen everyone agreed he said to EDi "Unlock our last conversation Spectre authorization kaidan Alenko."
"Wait you can lock EDI down? Why didn't anyone tell me that." Joker said slightly annoyed.
"Jeff, I agreed to it after Shepards clone took over the Normandy. It's to avoid any of their mission data leaking should anyone lock me out of the ship again.
Which reminds me kaidan, since Shepard is at least for the moment considered deceased, my protocols have transferred his files to yours. There are currently 517 reports and one personal message you can access." EDI looked at kaidan "Oh I see you should probably read the message wen you are alone kaidan."
"Wait," Liara blurted out. "Am I the only one who wonders why EDI the overly precise AI said at least for the moment considered deceased?"
"Now that you mention it, Edi must have a bug or something since we patched her up again." Tali started scanning EDI with her omnitool.
"It's alright you two, EDI works perfectly normal." kaidan then explained them why he believed it wasn't Shepards body.
After a long discussion they agreed on a course of action.
Liara had decided the best thing she could do is try and reactivate as much of the Shadow Brokers sources.
While Tali would go to the Destiny Ascension to help with the Geth reactivation. Though that was just a good excuse to set Liara up with direct information from the council.
Tomorrow kaidan would go and have a chat with Aria, pick up a body and hope she could shed some light on the situation.