Note: I love the idea of Atlantis as a live thing. I need to start writing longer stories.
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It was their first sign.
John had led a motley team through the city on the day of his discovery. New lights lit up behind him and new systems hummed under his feet.
It was a small room at the center of the city, walls lined with buttons, switches, displays, raw wire and crystal. Lights and working parts encrusted every surface like the creatures left behind in Atlantis' metal tidepools. Rodney stared around with a blind, amazed expression, tablet forgotten at his side. Weir and Zelenka had to help each other to the floor before they fell over.
John just smiled.
There was a raw place in the middle where chair might have been uprooted, and he sat there, crosslegged. When he closed his eyes, the city made a rumbling noise beneath him. "She's saying hello."
"Saying?" Rodney's voice was weak and strained. His hands fluttered around the walls, wanting to touch but never daring to go close. "As in vocal cords?"
When John laughed, lights flashed.
Much later, when the city is heaving and bucking, rejecting them, Rodney will remember this. He hears her groaning, screaming around him and he thinks organs, insides, and he screams with her
The city was in John's genes and under his fingers. They never knew she was in his head as well.