You know, I was working on a setting for a while that was a little bit like this.
Basically, Cyberpunk meets Biopunk. (Which actually exists and I hate whoever named that.) The molecular compilers used in the setting are modified cells (ProMat, programmable material) that carry out either genetic or electronic instructions, making parts and materials used for machines of varying sizes. They can also be instructed to multiply, self destruct, etc. Engineers basically mind-meld with the systems that create these instructions, called Architects, which are giant Folding @ Home clusters that can parse genetic codes and accurately simulate what will result, which allows anyone that knows how to use the system to take their design, plug it in, and have it put together a genetic code that will allow it to be grown. Not only that, the Architect could toy with organic DNA as well, though by comparison to machine genes it's more complex and less predictable.
A decade or two of injected implants and literal man-machine hybrids later, a virus couples with one of these ProMat germ cells and starts infecting a huge range of living things, mostly people, with a disease that mechanizes their bodies and nervous systems and then forcibly connects them to the Internet, which by now is a huge clusterfuck of AIs. The huge clusterfuck becomes huger. Also, an engineer did it, because he was a prick. (There's actually more to it than that but I'd have to drag it out more and I don't wanna.)
End result: Mutants, cyborgs, and the ongoing decline of the Internet into a sanity destroying hell. And the survivors of the age of transitions trying to make the world work again.