A/N: This is based on the synthesis ending (because I've done it twice) and it kept tickling my mind after I watched the EC DLC epilogue. Because I'm a huge Shenko fan (and I played through ME3 romancing Kaidan), this is told from Kaidan's perspective. However, it should fit regardless of who was romanced in the game.
Ghost in the Machine
He stood there staring at the names, a plaque tucked gently under his arm. It was a name he never wanted to put there and deep down, he knew that to do so was to perpetuate a lie. They all knew it. They all felt it deep within their bones, their souls that she was not gone.
Even now, several months after the Change had occurred, he could still hear whispers of her. Her quiet laughter—meant only for him—echoed through his entire being. Her reassurances soothed his heart.
He looked at the plaque bearing her name and looked back at the wall. Her name doesn't belong there, he thought. Even though he knew that he would never see her again—not physically, he also knew that she would always be with him. His lips quirked upwards as he realized that was what one usually said when a loved one died. But she wasn't dead... not exactly.
If anything, she created the world anew—and in her own image, he mused, recalling the extensive amount of cybernetics integrated into her body after Cerberus found her.
He looked at his comrades, all affected by the change she wrought. They know, he thought. They know that she did this for them. And she would do it again, he realized with certainty. She would leave him alone without hesitation, if it meant she could save them all. And she did. She saved everyone if the scant reports they had received were accurate. The Geth, Quarians, Turians, Asari, Salarians, and countless other civilizations—hell, even the Reapers—owed her a debt for her sacrifice. That's what they would say anyway.
But she didn't really leave.
He could hear her, and sometimes it seemed as if she was there, just outside his peripheral vision.
The others had mentioned it as well—sensing these ghosts of her.
He placed the name, running his fingers over the slick plaque, the intentions of her name, brushing the cool stone. He placed it, but it was a lie. She wasn't gone. She was with them every day, every moment, buried deep within their cells, but she was there.
He looked at EDI. She, the best of all of them, understood as he did. He hugged her then, whispering.
"This is a lie. She's still here."
"I know." EDI replied. "And she always will be."