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.

Intuition

John felt empty, something was different the moment they had left the Styx base. EDI told him it must just be because of the control signals proximity they had been in. But John knew there was something else going on, something no one had told him about, they didn't have to he would figure it out himself.

It had been the first time anyone had asked him to become his old self again. Coming from Kaidan it had to be important. John would see it through but he felt insecure nonetheless.

The second John had arrived on the Normandy with the first batch of refugees they had saved from the base he knew everyone had looked at him for guidance, now he had to be the Legendary Commander Shepard, even if it was just for these people.

John had walked past them towards Liara. Taking a deep breath he tried to seem as confided as possible. "Get me Aria on the line."

Liara smiled nodding slightly. "Yes, Commander." She said loud enough that the refugees heard her. Then she added in a whisper. "Crew deck, other side of the med bay. My VI will instruct you."

John felt grateful, the Asari had immediately understood that they needed to keep up an appearance. John took the elevator while a bunch of crew members ran towards the refugees.

When he arrived on the crew deck a small floating orb raced towards him. "Shepard I have Aria and Commander Bailey waiting for you. She is not amused."

"Ehm you're the VI Liara spoke about?"

"Yes follow me." The VI floated towards one of the rooms that he couldn't access earlier.

John breathed a few times really deep before stepping in the room. Whoever, whatever this Aria was. He had caught that everyone seemed nervous to talk to her.

"Shepard? Crap you look like shit." The blue strict woman said.

"Yes, Aria. I need your help." He had taken Kaidans advice to hearth to not show he didn't know who he himself or the Asari was.

"Hmpf, I already cleared my debt when I handed your pet that information." The woman waved him off.

"Aria I'm going to be honest with you. I have no fucking idea what you're talking about. But I need access to C-sec holding cells. These Styx fuckers are using innocent people to fight us." Shepard tried at his best big bad evil stare he could manage without laughing.

"Shit Shepard, the same fuckers that are bothering MY Bailey and his men?" The woman got angry, John wasn't sure if that was good or bad.

"Don't know Aria, but in case you heard of them... It seems these are the same guys as a certain group who called themselves Cerberus a while back." John didn't know what to tell her to convince her.

"Cerberus..." The Asari seemed disgusted. "Bailey will see to it that you have everything you need... And Shepard, be sure to destroy them this time."

"Thank you Aria, and I intend to make them disappear." John was honest he had only a few memories about them but it was enough to want them gone.

"Shepard, tell me what you need." A somewhat older man asked him.

"Pickup for a few dozen civilians. We have a Geth stopping them from attacking. They need screening if they have control chips and those who do have to be locked up until we can help them."

"I'll send over one of our new merc groups... The Guardians, their leader is Zaeed massani. Think he was part of your team back in the day." The older man looked at him suspiciously.

Glyph brought up a small console with a simple "YES" stated on it.

"Yes, but that seems ages ago." John tried to keep his expression neutral.

"Okay, he'll send his coordinates to your ship. And Shepard... It's good to see you're alive, Aria wouldn't admit it but she missed you to."

"Shit Bailey, You're fucking her?" John had a questioning expression written all over his face.

"Shepard... Don't talk about that, she could hear you." The man looked over his shoulder.

John laughed out loud. "Hey whatever makes you happy..." Bailey cut the connection, John grinned from ear to ear. He found the thought funny that someone like Aria would settle for a small time bureaucrat like Bailey. There was a hell of a story behind that.

John watched for the first time over Liara's room. He wondered why she had all the screens and equipment here.
"Say Glyph, what's all this stuff for?"

"We need this to maintain the shadow brokers connections." The white globe slightly bounced as it spoke.

"And the big sarcophagus next to the bed? What's that for?"

"That is the stassis pod containing Admiral Anderson's remains." The globe hovered over the big white box.

"Why is it here?" John couldn't comprehend why anyone would keep something like that in their room.

"When the councilors where aboard the ship we had to cover for the possibility that you had killed the Admiral." The white globe flew over towards a data station.

"Shit" John murmured under his breath and left towards his room.

Kaidan was feeling burned out, most of the day they had been running pickups to gather all the refugees and deliver them to the Citadel. Luckily Garrus had taken care of dealing with Zaeed, the two of them had secured a part of C-sec cells enough to keep those unfortunate enough to have become implanted with control chips.

Kaidan was trying to finish a report, he didn't know how he was supposed to explain this to the council. But he knew it was time to inform them on the latest developments. They needed to know that Cerberus was still around. They probably would even need to take extra precautions.

Being in command of a ship during a covert operation was taking its toll on him. He was trying to find a way to explain what had happened when an idea struck him.
"EDI could you connect me to my mother." If anyone would have good advice it would be his mother, even if he couldn't tell her the details. She always seemed to know exactly the right thing to say.

The image of his mother popped up on his workstation screen.

"Hi honey, how are you doing?" His mother took a sip at a strange glowing purple drink.

"Ehm, mom? I'm not interrupting you with anything important am I?"

"No Kai, nothing important. I'm just having a few drinks with some friends, we all wanted to heighten our spirits a bit." She looked genuinely amused. From behind her Kaidan could make out the low rumbling voice of a Krogan. "If you want to heighten your spirits you should pour some rincoll in that girly drink of yours." Kaidan heard someone else laughing in the background.

"No mom I didn't want to disturb you. I'll call back some other time." Kaidan was glad his mom was enjoying herself.

"No Kai, the others can wait. So did you find what you where looking for?"

Kaidan got serious for a moment. "Yes, but it's classified."

"Kaidan I know that look from you. Wasn't it what you hoped for? Is something wrong?"

Damn she always looked right through him. "He is.. It's complicated. He can't remember anything and..." Kaidan stopped talking when he suddenly recognized the person in the background. He saw his mother look over to the woman.

"Kaidan you have to tell her " His mother nodded over towards the woman who was suddenly looking straight at him.

"Hey specterrrrr? Nice that you... hicks... Call your mom at least..." Hannah took a large swill from the bottle of Batarian shard wine in her hand.

"Councilor Shepard, I ehm... We have to talk. Can I meet you tomorrow?" Maybe it was a sign that she was alone at his mother's house.

"Ssurrre Scepterrr, I'm here." Hannah stumbled away.

"Is she alright?" Kaidan wondered at what he just saw.

"She's fine, just a bit drunk. I think it's her way to cope with her sons loss." Emma looked a bit more serious. "Just come by tomorrow, I'll get her sobered up by then."

"Thanks mom, you're the best."

"I know Kai." She smiled as they said their good byes.

Kaidan now knew he only had to tell John he was going to meet his mother tomorrow.

John stood under the shower, letting the warm water wash away the dirt, pain and sorrow.

After talking to Aria John had retreated back to his room. He had wanted to look through the data Charles had given to him. It hadn't been pleasant to watch. Some parts he had remembered, the operations the painful torture. But there was one thing in there he hadn't suspected.

When he watched at the images again, some early stage of his time in the Styx base. The images where from when they had first woken him up. He had known who he was at that moment. It was only after he had attacked one of the doctors that they had kept him restrained and started experimenting on him. But it was the face of one of the people who gave the commands he now recognized.

For the moment everything he could do was let the water flow over him, hoping it would carry away everything. The bad memories, the horrible moments of his life. John couldn't stand it anymore, why was every memory that came back just one terrifying experience after another.

Who was the man he used to be, why would anyone expect him to want to be that person anyway?
John hit his hand against the wall, he was angry. Didn't this Commander Shepard have anything that would have been worth living at all? Was he only a pushing bag for the galaxy's most cruel and horrible villains?

He stepped out from under the shower grabbing a towel which he bound loosely around his hips. Staring in the mirror he was annoyed by his own appearance, yes it had gotten better. But the scars where still riddled all over his body. The red glow reminding him of the things that had been done to him. Chakwas had assured him they would be gone within a few days, but she could only hide them. He knew they would still be there just hidden.

Someone knocked on his door, he didn't care whatever they wanted it would just be another reminder of a man he didn't want to be anymore.

Another knock followed, John didn't want to be disturbed he wanted to be left alone. He hit out, this time his hand flew straight in to the mirror. Shattered pieces flying through the room. His hand was bleeding, some shards still sticking in his hand.
Blood flew in a thin red river down the drain, the pain of in his hand gave him a kind of peace he hadn't felt for a some time. A memory came back scratching on the edge of his consciousness.

"John?" Kaidan yelled in the room Before stepping inside.
Kaidan knew John was here, but it worried him when he didn't answer the door. After a while he had ordered EDI to open the door for him. When he heard the water running he was about to leave when the bathroom door slid open.

John stepped out, only covered by a towel and still dripping wet. Blood flowing from his hand, he had a grin when he held his hand up.
"The mirror was tougher then I thought." John chuckled as if he had to laugh at himself.

"Oh god John we need to take care of that." Kaidan slipped past John and grabbed a towel. Shooting a questioning look towards John. "What the hell did the mirror do to you?"

John closed the distance between him and Kaidan.

Kaidan tried to grab John's hand and press the towel against his bleeding knuckles. But John suddenly grabbed the back of Kaidan's head pulling him closer. He was staring in Kaidan's eyes, with a questioning look written all over his features.
"What is it with you Kaidan? What is it you aren't telling me?"

Kaidan blinked. "I don't know what you are talking about."

"Kaidan I know you keep things from my past a secret. What I want to know is why?"

"John we should really take care of your wounds you're bleeding all over the place. You should probably go to the med bay."

John shrugged. "It's not that bad, I think the mirror is a lost case however."

Kaidan grabbed a first aid kit and pushed John back out of the bathroom. "Sit on the sofa, at least let me pull out those shards. Then you're gone tell me why a mirror deserved to die."

John sat down holding his hand out towards Kaidan, who started to clean out the wounds.

"So what was the mirrors mistake? Just asking so I know what i should avoid in the future."

"I just got angry, about everything and nothing really. But it's better now." John starred towards his feet.

Kaidan rubbed some medigel on the wounds and made a bandage to cover everything up. "Okay as you doctor I suggest to avoid getting angry at mirrors in the future."

John looked in to Kaidan's eyes, a feeling scratching its way to freedom.
"Something deeper with someone I already - care about"
Suddenly his hand grabbed the back of Kaidan's head pulling him closer. John closed his eyes, pressing his lips on Kaidan's.

Kaidan was surprised, it took him a second to realize what was happening. Warm lips finding his, a strong hand held him close. It was just like it had been in his strange dreams. But before he could really enjoy what was happening John had pulled away.

"Shit, I'm sorry I don't know what came over me." John turned his head away.

Kaidan grabbed the other mans shoulder. He could feel the strong muscles under his hand tense. "John look at me it's okay, really."

"No it's not, I don't know why I did that. It's just... I.. crap."

Kaidan forced him to turn around.
"It's okay John, I understand."