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FIXME A better description is required.

The nano-plague somehow prevents nanites from working properly.

The techbase that created the nano-plague is >= a few tens of millions of years beyond humanity's. (Invocation of Clarke's third law)

The nano-plague was created by entities that A) were sufficiently advanced that UtCS-era extant species still can't figure out how the things really work except in broad characterizations (forms colonies, probably has collective AI capabilities, reacts violently to attempts to eradicate it, individual entities operate from unknown power source, etc.) and B) apparently didn't consider most (note, not all) organics to be a target.

See also