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.
Hades
Kaidan was working through the data Liara had gathered. After they had finally found Shepard the leads where somewhat easier to follow. It seemed that Without Shepard Styx was a whole lot less organized, at least the 2 mercenary groups that attacked some food supplies in the last day hadn't been much of a challenge for the Alliance forces.
EDI was trying to triangulate the base of operation from styx by collecting all data they knew Styx had shown themselves. Though it was a slow process verifying the real appearances of Styx. Some of the attacks and recruitment they had seen came from petty criminal organizations.
Kaidan was trying to find anything that could get them a bit closer to stopping Styx, if John could only remember where they had taken him. But apparently Styx hadn't entrusted him with the locations always them secret. If only Shepard where here, the old Shepard, the one who had an answer to everything. The one who faced down collectors, rogue spectres, reapers and Cerberus.
Not just the confused person he was reduced to since someone screwed with his mind and started calling him Deimos.
Wait why would they call him Deimos anyway?
"EDI, give me a search on everything called Deimos."
"I have 4.698 different entries for the word Deimos, do you want to narrow your search Kaidan?"
"Deimos referring to Human society or culture."
"I have Nine entries remaining; sanctuary to the Ice Warriors in the fictional Doctor Who universe, son of Ares in Greek mythology, a villain from a 20th century comic book series..."
"Wait stop, Greek mythology? What's that one about?"
"Deimos, son of Ares and Aphrodite, also meaning Dread and known as the personification of Terror."
"Wait Liara's data contained something about Styx and Greek mythology."
"Yes it did Kaidan, the river Styx also meaning "hate" and "detestation", the river that separates Earth from the underworld."
"EDI one last question, Cerberus and Greek Mythology?"
"Cerberus or the Hellhound which guards the gates of the Underworld, to prevent those who have crossed the river Styx from ever escaping.
Kaidan we seem to have missed the obvious."
"Yeah, well now that we know who where are dealing with this is going to become a whole lot easier." Kaidan paced through the room. "EDI, see if we can find Miranda Lawson, if this is a new version of Cerberus she should be the closest thing to an expert for Shepard's implants we can get."
"We should ask Liara to use the Brokers network, the Broker had information on Miranda's activities."
"Good, I'll talk to her and inform the crew. EDI compare every bit of information we have on Cerberus to the activities from Styx."
Shepard was restless, since the tranquilizers had worn off he didn't know what to do with himself. He had sat hours staring at the items in the room. He liked the ship models, EDI had answered every question he had asked, ship types from the models, where the chessboard came from. But nothing meant anything to him.
He had spent some time walking around the ship, but it was making him uneasy. Everyone seemed either to avoid him or disappointed that he couldn't remember them. He had heard some of the crew speak about his appearance, even here it seemed everyone was disgusted by the bright red scars.
He hadn't found Kaidan anywhere but EDI said that the primary staff was in a meeting in the war room. One of the few places he couldn't go without an escort. So in the end he just returned to his room, the only place where he didn't have to endure being stared at.
He had tried sleeping but the giant window above the bed made him uneasy. Something made him panic whenever he looked in to the wide empty space outside. He had searched for something to keep him busy, the answer had been a large box filled with pictures and letters. He wondered who they where from and why they where stored here.
Kaidan had been sitting in the mess hall for hours, he wanted to go and see John. Just he didn't know what to say. "Hi, I know you don't remember me but we where secretly in love and never had the chance to be together?" Yeah not really a great conversation starter. He had hopped he would just accidentally bump in to John while he was exploring the ship. But from what EDI told he had done that while Kaidan was in the meeting.
Charles walked up to Kaidan, cocking his head slightly to the side. "Alenko Major, we have a question about human behavior. EDI said it was best to ask one of you."
"Ehm sure Charles, what do you want to know?" Kaidan grinned he remembered Shepard mentioning the times where EDI had questioned him about all kinds of human behavior.
"What reason could humans have to cry when they are not in pain?"
"Depends there are a few, if we are really happy or sad, sometimes if we are desperate or just remembering something bad. Why do you ask Charles?"
"Shepard Commander seems to be under a lot of stress, he is crying, we do not understand he was only looking at pictures."
"I'll go check on him."
Kaidan ran to the elevator, why can't these things go any faster. When he finally arrived on the first floor he paused for a second before knocking.
"John? Everything alright?"
No answer, he knocked again. This time he heard a murmured "come in" from behind the door.
John was sitting between a pile of pictures trying to cover up that he had been crying. Kaidan quickly grabbed the box of tissues from the desk and moved in front of John. Holding out the box for him.
Shepard grabbed the box without looking up, only staring down embarrassed.
After a few minutes John took a deep breath. "You gone keep staring at the freak like everyone else?" His voice was soft, a tone of resignation swinging with every word he spoke.
"What freak? I see only one of my dearest friends who needs me to be there for him." And the man I love Kaidan said to himself.
John snorted. "Yeah right, most avoid me, can't even blame them I look like a monster."
Kaidan reached out lifting John's face with one hand. "I see no monster here, the ones who did this to you on the other hand. They are the real monsters, but you? Shepard those are only scars, scars can be healed."
"They said it's impossible it's who I am." John turned his eyes away from Kaidan.
"Who said such a thing?" Kaidan's expression changed to disbelieve.
"Phobos, he had a similar scaring."
"Shows what he knows, you want them gone? No problem, I'll see to it that the doc takes care of them tomorrow." Kaidan shrugged. "But somehow I don't think that was the reason you where sad."
"No it's... Everyone expects me to be someone they know. Some are even angry i can't remember who they are. The pictures, the letters every single one of them is about a man who did great things, someone who saved everyone. How am I supposed to fulfill those expectations?"
Kaidan sat down next to John, taking a moment to breath before he turned and faced John. "I never understood how you managed it all. Heck I'm in command of this ship for a few weeks and i feel like I'm drowning in work. Whoever expects you to be that man again." Kaidan pointed at the pictures."Well he will have to fight his way past me."
John smiled a little. "You? If I remember correctly you only defeated me because you where using a sniper, a krogan and a bunch of marines against me."
"You're forgetting an old lady with a syringe in that list."
"Yeah that was mean, I mean come on you know I don't like doctors." John suddenly became very silent.
"I would almost believe you. If I didn't know you had amnesia."
"No really I don't like them, especially the one with a love for scalpels" John started trembling. "I remember the labs where they kept me, they where doing... something... to me. The doctors reported in to Phobos... Phobos he told them to make me obey."
Kaidan put his hand on Shepard's. "John they can't touch you here, I promise we will make them pay for what they did."
John started crying again, the memories he was reliving at that moment where to much for him.
Kaidan put his arm around John's shoulders, just holding him. John turned and let his head rest on Kaidan's shoulder. The wet tears soaking his shirt it didn't matter John needed him. Kaidan would embrace him for all eternity if it would help John.
After a few minutes John lifted his head. "I'm sorry i didn't mean to."
Kaidan smiled. "I'm here if you need me, John." Kaidan nodded towards the bed. "You should probably sleep and tomorrow everything will be better."
"Could you ah... stay for a little while... I mean if it's not to much..." John said barely a whisper.
Kaidan swept the pictures and letters from the bed, kicked of his boots and held back the sheets.
"I told you I'm here for you."