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.
The One Ring
John kicked off his boots the second he had reached his room on the Normandy. That last talk with his mother had left him somewhat conflicted over his own situation. He wasn't sure what to think of this new development, on the one hand he was glad that once again being a spectre would give him some protection from being hauled of to the Alliance for questioning. But on the other side there now once again where people depending on him to be the Commander Shepard he used to be.
John sat down at his desk if he was going to be a spectre he might as well use his new rank to gain more knowledge about everything going on around him.
"EDI unlock all special reports from Commander John Shepard."
"I transferred all files to your personal workstation, Kaidan moved authorization of your former files back to you Commander. I also took the liberty of restoring your access to all security footage from the Normandy."
"Thanks and EDI.. It's still John, not there yet."
"Yes John, also DR Chackwas wanted to remind you that you should come in for your last treatment."
"hmpf, forgot about those." John said more to himself then anyone else.
A few minutes later he had at least gained a small overview of the data he could now access. Most where old mission reports, John quickly transferred them to a data pad. If he had time he would read through those later.
But a single file caught his eye, it was dated after his spectre codes had been disabled.
John opened up the file labeled: where it all began, there was only a single image in the file. A ring with an inlaid stone, on the inside there where names he didn't recognize on the stone there was a single word written.
"RIO"
John looked at the image for a while. He had seen a ring like that recently... On Kaidan's dog tags.
"EDI, who sent this file?" John pointed at the monitor well knowing that the camera in his room was still in place.
"Untraceable, Whoever sent it knew how to hide it from me." The disembodied voice sounded through the room.
"Where is Kaidan?" John transferred the image to a data pad.
"War Room"
John ran towards the elevator, he was sure the image meant something important. He just wasn't sure what it was yet.
"Major, we can't find any trace of Miranda Lawson. We know you need her for your mission but we can't find her. She disappeared after the war was over. But if you tell me what you need of her, I'm sure we can find an adequate replacement."
"Admiral, I'm sorry I can't tell you anything more about what we are doing at the moment. Miss Lawson is the only one who can help us at this point."
"Damn Alenko, What the hell are we supposed to do? First a missing corpse, then all this red tape and the only thing we hear from the Normandy is a short Cerberus is back. Even the council won't tell us what's going on."
"Sir I understand but I can't change anything about this. I can only discuss the details with the council."
"Then at least tell me what's this about a new human Spectre?" Hacket sounded annoyed.
"That's as classified as it can get, sir. The council made it clear that no one should know who this new Spectre is." Kaidan was getting tense he could tell that the Admiral wasn't about to let it go.
Charles walking up behind Kaidan however was enough to distract the Admiral for a moment.
"Alenko Major, the Redacted designation Spectre. Requires your presence." The Geth's head turned from Kaidan towards the Admiral. "Hacket Admiral we must request to stop asking question regarding the identity of Redacted designation Spectre." Charles slowly turned and left.
Kaidan watched ow the Admiral stared at him in disbelieve. "Sorry Admiral but I need to go." Then he cut the line before the Admiral could reply. Slowly turning and moving back in to the war room.
John stood there with a large grin next to Charles. "How was my Geth impersonation?"
Kaidan shook his head. "That was you? How?"
John leaned back against the wall and shrugged. "I've been training with Charles, the whole control chip thing... Anyway I can use the Geth consensus now, guiding his actions. Maybe we can use it against Styx one day."
"Well I'll be damned, not that I'm not grateful for you saving my ass from Hacket but still it's hard to wrap my head around. Anyway did you need me for something?" Kaidan blinked his eyes when he saw the Geth next to John imitate Johns exact movements.
John leaned over to Kaidan giving him the data pad. "I got a message, someone directed it at me knowing my spectre codes and the Normandy well enough to hide it from EDI and Liara. Take a look."
Kaidan watched the single image displayed on the data pad, his hand moved unconscionably towards the chain with the ring.
"I thought I saw that ring last night. So what's the story, any secret lovers i should be afraid of?" John took two paces towards Kaidan pulling out the ring from under Kaidans shirt.
"It's yours, only a handful people knew you had worn it on the chain of your dog tags, even less knew that there are names on the inside." Kaidan grabbed a small chain with two dog tags from the table in the middle of the room. Placing the ring on the chain he held in his fingers. "Here I didn't have a chance yet to give them to you, now that you're reinstated."
John took the chain containing the dog tags inscribed with his own name. Studying the ring. "It doesn't look that special." He hung them around his neck and slid the ring under his shirt.
The second the ring touched his chest, John dropped to the floor. Charles leapt forward-looking at Kaidan. "I lost the connection to his control chip." Charles grabbed John and started running towards the med bay. "EDI we need Medical assistance."
Kaidan didn't even realize what happened, all he knew was he had to run after the Geth who was carrying John.
Death
Destruction
All the images he saw flashing in front of him overwhelmed his senses. He couldn't understand them, the images confused him. There where only a few moments they seemed clearer. In those moments he could see himself, laughing, crying, dieing, Fighting.
"Doctor what's wrong with him?" Kaidan was impatient, he couldn't stand waiting anymore.
"Physically he's fine. But I detected some unusual brain activity, abnormal beta waves. Otherwise there is only an increase in his rapid eye movement, signs typically associated with intense dreaming." The moment Chackwas finished talking John opened his eyes.
"What? Where am I?" John rubbed his eyes as the light obscured his view.
"John you dropped to the floor, I was worried something happened to you." Kaidan grabbed John's hand.
"I'm fine, just some strange dreams. Doctor how long was I out?" John sat upright on his bed.
"Only a few hours. Your condition closely resembles what happened at Eden Prime. I need to look in to this." Chackwas wandered off.
"John I was so worried." Kaidan grabbed John's hand tighter.
"Kaidan I'm fine, really." John squeezed Kaidan's hand back. "Doctor when can I leave?"
"I should consider keeping you here, normally we have to force you to stay here. Since you asked nicely I would say let me finish up some tests and you can return to your cabin later. I will be keeping you under close observation off course."
A few hours later John was sitting in his cabin waiting for Kaidan. John was still pondering over the ring and the image that was sent to him, what was in Rio, why would someone sent him such a message? Who could know he was onboard the Normandy and would be reinstated as a spectre.
The door slid open and Kaidan came in. "Hey, I didn't even have to knock or hack the controls what's going on?"
"Nothing I just thought since a simple security protocol won't stop you from entering I could just as well give you full access to my room." A smile darted around John's lips.
"And here I had just gotten used to overriding your security every time I wanted to come by."
"Should I lock you out so you can sneak in on me showering?" John lifted an eyebrow.
"Nah, I could just drag you over to the shower." Kaidan slightly tilted his head towards the bathroom.
"Wouldn't say no to that." John jumped to his feet grabbing Kaidan, bending him over for a kiss.
Their lips and tongues found each other in a familiar way, guided by the need to be together. Hands wandering over each others body's searching for something to hold on to. John leaded Kaidan towards the bathroom door pulling Kaidan's shirt out from his pants, so his hands could feel the soft, warm skin beneath.
"Commander your blood pressure and hart rate increased, is everything alright?" Chackwas voice sounded over the intercom.
"Shit." John murmured under his breath. "This isn't going to work if she's watching."
"Sadly no." Kaidan let go of John pinching his ass before letting his hands be drawn away of the object of his desire.
"Everything is fine, Just working out." John replied pushing the button on his desk.
"I would advice against that for the moment."
"Okay, doctor I'll do something else than." John cut of the communication before she could comment.
"So? Now what do we do?" Kaidan straightened out his clothing obviously disappointed.
"Ever played Biotic Chess?" John pulled open a drawer.
"Never heard of it. What are the rules?"
"It's like chess only we move larger objects through the room with Biotics. The goal is to hit your opponent with one of them." John pulled out a key and opened the display case to his model ship collection.
"You're making this up."
"Maybe I am. But there must be a reason I have all these miniature ships. You get the Geth, reapers and non council races. I take the council ships." John grinned as he laid out the ships on the floor. "Now a ship that gets hit is out of the game, you have to break to your opponents defenses before you can attack the player."
"Okay, let's try this. Maybe you just invented a new strategy game." Kaidan took up his position between the bed and sofa.
"Traynor would be so angry she can't play it."
During the next few hours both of them spent refining the rules, dodging attacks and finding new ways to use their biotics to move ships across the room. Until both of them where tired and fell asleep arm in arm.
The Shutters on the ceiling window opened Filling the room with a soft light. A song sounded through the comm system, Kaidan slowly opened his eyes needing a moment to gather himself. "The Girl from Ipanema? Really Joker?"
"Sorry Kaidan but you said to wake you before the sun went up over Rio, the song seemed appropriate."
"Be careful Joker someday you might regret it."
John opened his eyes smiling towards Kaidan. "Still here? Thought you would have left me for someone more interesting by now."
"Never, anyway I should prepare. Today We find out who sent you that message." Kaidan swung his legs over the edge of the bed.
"So what's the plan?"
"I go down together with EDI to deliver James to the N7 program on base in Rio, your mother speeded up his paper work. While we are there we try to find out who sent the message. While he checks in for training I try to distract anyone who could ask questions while EDI tries to trace where the message originated from. If everything fails, James can still send us anything he finds out while in training"
John thought about it for a moment. "I should come with you."
"You can't, the second you set foot on an Alliance facility every marine will recognize who you are. If Styx is there they will pack up and run."
"Styx knows who you are they would set of every alarm bell the second you enter."
"Probably, that's why I want you and Charles in the shuttle. If they run you follow them. EDI can maintain contact with Charles. Liara will stay here to assist in going through any data we find."
John stood up and flexed his muscles. "Okay but I get to take Garrus." John walked over to his armor closet.
The shuttle had been cramped with the six of them in the back. Steve had landed them on an open field inside the base.
"Check in is in the main building, the N-Program is located in the back of the base." John pointed on the map on the display.
"Loco any last advice?"
"Yeah hands of my records or I'll need to come back and break them again."
James laughed as he picked up his footlocker and stepped of the Shuttle.
John put in his earplugs listening in on Kaidan as he talked to some soldiers on the reception. They waited for a while where nothing seemed to happen. James paperwork was checked and he was being entered for training. kaidan was chatting up some officers who seemed all to happy to talk about their work now that the war was over.
John sank a bit deeper in his seat, while he listened how the officer bragged about how they rebuild most of the base already and how nice their new recruitment plans where going. James was sent of to medical examination, just as John thought he would fall asleep Charles informed them that EDI had acquired access to the database.
"Anything useful?" John watched as the Geth read the data streams on a monitor, too fast for the human eye to follow.
"Massive amounts of communications, but those where to be expected. We are sending everything to the Shadow Brokers network, the broker will cross examine if anything stands out." The Geth didn't move his head away from the flashing screen.
"This is useless by just sitting here we will never find out who sent that message." John was restless from all the waiting.
"EDI has been noticed, she is fighting of the security protocols. John we need to get them out of there before anyone notices."
John nodded opening the communications to Kaidan. " Alpha team, retreat the cat is out of the bag." No reply, Kaidan's communications where down. "Kaidan? James? Can you hear me?" John loaded his guns and put on his helmet.
"Suit up people we must get them out of there."