Ooooh I like all of your ideas! Yeah, I originally had the virus be this thing that was created by the machines to force them to convert. Maybe the leaders were the ones that made it to push their machine agenda all along. 

Jacob will basically be controlling Matax in a VR kinda doohickey thing, but once he becomes disoriented, Matax will either go offline, or go into autopilot. I'll try and come up with some random names for the disease and we can hopefully mix and match what we brainstorm. 

I like the idea with the first post having both of them together on the fortress. I'll be sure to add the dramas.