Nanobots are a good idea! I was originally thinking of toxins, but those could be released by the nanobots
I even managed to figure out why the nanobots are attacking: they use the matter from the cells (and virii, and prions
) to build more copies of themselves. The Pathogens and the Macroscopics (body cells) sign an uneasy truce to fight off the new common threat. What would be some of the skills some of the microbes could have?