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.
Deimos
"Hey Kaidan."
Someone shook his shoulder.
Kaidan groaned he didn't want to wake up it was warm and cozy. But the soft voice was relentless.
"Kaidan come on, I need to show you something."
"What is it John?." Kaidan turned his head towards the voice, slowly opening his eyes.
"Ha there you are, you need to see this Kaidan."
Kaidan only slowly recognized his surroundings. A large bed, Shepard was standing over him, the ceiling window showed a perfect view of Mars. In his arms John was silently snoring.
"Wait what? How?"
Shepard laughed. "You fell asleep holding him, I didn't want to disturb you, but you really have to see this."
Kaidan took a closer look the standing Shepard had blue eyes, the man in his arms was covered with scars.
"So why can I see him here?" Kaidan was confused.
"Because he and I are one, he just can't remember." John held out his hand.
Kaidan grabbed it and saw himself being pulled away from the other Shepard. "So what did you want to show me."
"Something beautiful." John pointed at a small moon in front of mars. "See that one, in a minute we will be in the perfect position then Mars and it's two moons will be in a perfect alignment."
Kaidan watched as a small, misshapen moon moved in front of the larger one in the background. Until the larger one wasn't even visible anymore. The reddish glow of mars dancing over the edges of the small moon. Kaidan was surprised when John pulled him in a tight embrace. He felt John's breath on his skin.
"You know I wish I could just wake up out of this here and..." John whispered in Kaidan's ear.
Kaidan pulled back a bit, a challenging look crossed his face for a moment. "Oh and what would you do then?"
John laughed loud. "You'll see one day, first he needs you Kaidan." John pointed to the other Shepard on the bed.
Kaidan sighed."I know, it's just. I don't know how to help him."
Shepard looked up towards the moons. "See that small moon? That's him, he needs to make the large one disappear. Just ask him how he would have gotten back to the base"
The large moon disappeared behind the dark side of Mars.
Kaidan grabbed the back of Shepards head, their foreheads touched. "I'm waiting for you to return."
"I know, but you must help him to become whole again first."
Kaidan held on to John, they kissed until Kaidan thought he would suffocate. John whispered against his lips. "You know this isn't real, you don't need to breath."
An alarm sounded, Shepard was alone in a dark room. His instinct told him to grab his helmet. Pipes bursting around him.
"Shepard" Someone yelled behind him.
He turned around, he knew he should recognize the person behind him but he couldn't put a name to the figure.
John ran through a ship, it reminded him of the Normandy, no he told to himself. This is the Normandy just a different one.
Suddenly he was weightless, drifting in space. His suit had a leak, the air rushed out of his lunges. He tried turning around, seeing a ship with a massive hole in it. His saliva started burning his tongue, his skin felt swollen and then everything went dark.
John was sweat soaked when he suddenly awoke, the wide open dark space looming over him. He couldn't bare the sight of space, panic befell him. He Pushed the arm that was holding him away and ran towards the bathroom. Anywhere was better then here. He needed a secure place, somewhere without windows.
"Kaidan he needs you." Shepard said sorrow written allover his features.
He took a deep breath, Kaidan didn't want to leave this place. The place where Shepard was, where they could spent time together. "I want to stay here."
"I know Kaidan but he needs you." Shepard let Kaidan go, releasing him from their embrace.
Kaidan watched over empty bed, John wasn't sleeping there anymore. One second later Kaidan awoke, hearing the shower running.
"EDI time?"
"4:30 AM standard Sol cycle."
Kaidan stood up, still a slight confusion about what just happened. He remembered a dream, something he needed to do.
Slowly he walked towards the bathroom, the shower was running. But he could hear a soft whimpering through the door. Kaidan took a deep breath remembering Shepard from his dreams. "John, everything alright?"
There was a moaning sound coming from the other side.
"John I'm coming in, okay?" Kaidan said before he unlocked the door. John was sitting in the shower the water running. "John what's wrong?" Kaidan made two large paces and knelt next to the man hunched in the corner.
Two large red eyes looked up to him. Horror was written over his features, something must have upset him Kaidan thought.
A soft uncertain voice whispered. "I remember dying in space." John's eyes where questioning him, asking him to tell him something else.
Kaidan sat down next to John, the water soaking him, he didn't care. After a few moments he looked back at John. "Yes you died, but that was over three years ago."
John's eyes grew wide He couldn't believe what he heard. How could he have died but still be here.
"Then why am I alive?"
"John you where revived by a organization called Cerberus, probably the same one that calls themselves Styx these days. It took them two years to restore you, then they wanted you to hunt down the collectors. EDI can probably tell you more details about that, she was around back then."
"Okay, so that was three years ago, how did I end up with them this time?" John was trying to grasp how anyone could die in pace and return from that.
"We don't know, maybe someday you can tell us what happened. We only know that you where wounded, loosing blood. But the rest we can only guess at what really happened."
John sat there for a moment trying to process the new information. But a new question scratched it's way to the surface. "Kaidan? Why are you doing this for me? I mean, I appreciate that you stayed with me last night and talked to me. But why go through all of this?"
Kaidan was taken unprepared to that question, he didn't know how to answer. He thought a bit over it and decided to tell a version of the truth. "I failed you when you came back to life, I gave up on you because I mourned your loss and couldn't believe you returned. This time I won't leave you, I will be here for you."
John held out a hand to Kaidan. "Let's go I want to leave this shower." He smiled, "maybe I can't remember who I was, but I know what I want right now. Breakfast."John stood up and pulled Kaidan to his feet. "Okay and maybe I need a change of clothes."
Kaidan snorted. "Yeah, sadly mine are in the crew quarters. I really like explaining why I'm dripping wet to the crew..."
A knock on the rooms door interrupted them, a artificial voice was heard. "Alenko Major, we brought you some clothes."
John looked puzzled.
Kaidan started laughing. "You remember that you are under observation? It's not only EDI who sees all, Charles here sees a few things to." Kaidan opened the door.
Charles cocked his head slightly. "I believe the correct human expression is: You look like something the cat dragged in."
"Thanks Charles, hope everything is alright?" Kaidan threw a knowing look towards Charles.
"It is now, Alenko Major." Charles turned and went away.
Hannah was reading through piles of reports, somehow it felt that for every problem they addressed 10 new ones arrived. It didn't help much that the new mercenary group had it out for alliance outposts, short of attacking ships directly they seemed intend at cutting down every supply line there was.
Ever since Major Alenko had arranged for the council to take cover among the Turian fleet it seemed they had more and more problems contacting Alliance command. A storm was brewing, Hannah could feel it in her guts. It hadn't been a good sing when the Major had decided to send his own mother to her for cover. She just knew there was something wrong with that, why would he use his own house to lure the mercenaries out? It didn't make sense.
But whatever the Normandy crew was doing it had at least put a dent in the efficiency of the mercenaries. Yes they where still a pain to deal with, but now they weren't half as organized. It seemed that a lot just resorted to standard scare tactics.
Hannah called her new friend, she needed someone to talk to once in a while and the Majors mother seemed content on just talking, no questions asked about her work. No words of sorrow and insincere condolences about Hannah's son. Emma was the only one who just seemed content with how things where, the woman looked towards the future not dwelling on the past. Hannah was just happy she didn't have to justify why she wasn't mourning, but the truth was she couldn't quite grasp it all. Her son had died, returned and died again somehow it all just seemed unreal.
"Emma, you have some free time? I need to get away from work for a while."
The woman smiled over the vidcom. "Sure, say why don't you come by my place for a while."
"Hmm, I have to see if I can get it past security." Hannah had something more in mind like Emma coming by, but maybe a few days on earth would give her a change of perspective.
"Don't worry about security, I have a nice lieutenant here who's mission is to guard the place. Also councilor Urdnot Wrex still has his Krogan buddy at my place."
Hannah shrugged. "Well then I would love to come by for a visit. Maybe you can teach me that apple pie recipe."
Kaidan paced in front of the med bay, John had been in there for hours. He had personally called the doctor out of her bed in the early hours, John wanted to have his scars healed and Kaidan was going to force everyone to just make it happen. He didn't even know why he was nervous about it all. Karin had assured him that it wouldn't be much of a hassle, just time intensive.
Charles was sitting on a chair reading a data pad, well more like downloading every book on the data pad in his consensus. Sometimes the Geth even asked questions. Last he was working on Human philosophy, Charles seemed amused by the big questions of life, why are we here, where do we come from. The Geth seemed even to try and find answers to questions he had.
Kaidan wondered if the big difference between the reapers and the Geth wasn't the simple fact that the Geth wanted to learn and evolve, while the reapers had wanted to preserve a status quo.
The doors to the med bay slid open, John smiled the moment he saw Kaidan standing there.
"She said it would take a few more treatments but in a few days the scars should be gone." He embraced Kaidan, pulling away after a few seconds seemingly embarrassed. "I'm sorry I don't know why i did that."
Kaidan felt relief, the man finally seemed genuinely happy. "Don't worry about it." Kaidan put a hand under John's chin appraising the work Karin had done. "Looks really good, I told you she can do it."
"Yeah seems like Phobos is a big fat liar." John was smiling from ear to ear.
Kaidan grew serious, Phobos... Where had he seen the name before. Something was up with that. He knew there was an answer there. "EDI, I need a search on Phobos relating to Greek Mythology."
However Charles was the one who answered. "Phobos, personification of fear, Son of Ares and Aphrodite. Twin brother to Deimos. Also an interesting fact While Mars is named after the roman war god the Mars moons are named after the Greek twins. I just finished analyzing Greek mythology."
Kaidan's jaw dropped down, he understood the dream he had last night. John was Deimos, he had to defeat Phobos. "Charles, I need an image of the moon called Deimos."
Charles opened a small projection on his omnitool and there it was the small not quite round moon.
John looked at him nonplussed, as awaiting an answer.
Kaidan couldn't believe it when he looked over to John a single question forming on his lips. "How would you have returned to base after the mission?"
John looked at him not really understanding the purpose of the question. "I would have said the passphrase. Struldbrug needs to return to the Brobdingnagian so be Swift."
"Charles anything you can help with?" Kaidan hoped the dream would hold an answer once again.
The plates around the giant light on the Geth's face shifted their position. "Struldbrug are immortals, Brobdingnagian means usually something of colossal size. Oh interesting, both terms originate from the same book, Guiliver's Travels written by Jonathan Swift."
"So nothing that helps us find their location." Kaidan was a bit disappointed.
EDI interrupted. "I might have something Kaidan, there was an old Cerberus facility in the Swift crater on Deimos."
"Now you tell me?" Kaidan snapped at the AI.
"It was only listed as the facility at Swift, only now could I link it to this specific moon."
"Get me Satellite pictures from the crater, I want everything on movement in and out of that sector from the last few weeks." Kaidan felt they where close, he thanked Shepard for giving him the hint in his dreams.
Note: So in case anyone was wondering...
Yes the cover image is a photograph of Deimos (moon).