I like the idea of an optogenetic infection. A bit like the cool trick used at one point by the protagonist in "A Quantum Thief". Suddenly certain light patterns become dangerous. If this had been a merely biological infection, then it would have been hard to have an effect on synths. But you said it was nano: the nanomachines might do something *different* against synthmorphs. A simple idea might be that they infiltrate some of their optronics and hence induce the cyberbrain equivalent - other impairments, sudden spasms when exposed to bright light, chameleon suits going crazy and flickering information that is picked up by nearby chameleon suits and cyberbrains. A more poetic possibility would be that the nanomachines help manufacture modified bacteria that eat the fiber optics - the biomorphs get infected by something artificial, the synths get infected by something biological. Of course, anything that starts messing with electronics is much more dangerous to a habitat than just a biological infection. Important systems will start to malfunction: first just exposed sensors, bots and home electronics, then increasingly key life support systems and finally controlling AI and power. This might be the real target of the infection, something the luddites didn't know about. Or, if you want to avoid it, assume the nanomachines are programmed not to attack non-synthmorph electronics (it recognizes the materials).

Nanomachines with physical control over bio- or cyberbrains can do all sorts of things, but presumably there will be some tough safeguards against such a thing - alarms would be raised if it happened across a whole habitat. But once they are in, they can do all sorts of bizarre and nasty things. Self-evolving nanoweapons sounds like a wonderfully bad idea - just the kind of thing that gets Firewall involved. An interesting question is who was actually behind it and why they choose to launch it - desperation, general desire to cause maximal trouble, or thinking that while everybody are trying to save things over *there* nobody will notice something over *here*? The Quantum Thief is probably a bit "the deep end of the pool" - very good, but doesn't pause to explain minor details like uploading or what happened during the singularity. I think "Accelerando" by Charles Stross might be a better place to start.

I would suggest that you use more than one set of possible hostiles. Some may be bluffs. Some may be potential allies if treated correctly. It makes life much more exciting for your players. With that in mind, I'd set up your Luddites as a 'wrecking crew' who were targeting Synths or Uplifts or blatantly transhuman morphs rather than the station itself. If they're Luddites, have them use nice, traditional systems. Fire. Explosives. Guns. Then have a vigilante set that's killing Flats they suspect to be Luddites. Then bring on the nanites and threaten station life support and have the players unsure of whether it's the Luddites or the Vigilantes. The thing releasing the nasty nanites might be either a hypercorp or criminal group with major issues with whatever group is running the station, and for bonus points you could have the nanites be a 'blackmail' system. "Okay, you all saw what happened when the pretty girl got the nanites. Give me what I want and I'll give you the code to tell them to stop." Or worse, it might someone who slipped through the anti-TITAN protocols who was infected with something really bad. But be careful about using that. That's the big thermonuclear weapon of the game system, it's kind of like actually bringing Cthulhu on-stage during a Call of Cthulhu campaign. Wherever possible, introduce more grey-areas and more potential hostiles and make the players have to figure out who needs their attention the most. It makes things far more exciting than a giant sign saying "Reward for hym who slays yon dragon." and another giant sign saying "Dragon in this cave." For bonus points, involve some of the player's corporation/clade contacts and make it unclear if perhaps one of THEM might be partly responsible for some of the crap being stirred up. Bring in those loyalty grey areas! Just some random thoughts.

One of the things I find most enticing about the idea of running an EP campaign is that it's sort of a horror game, like Call of Cthulhu. If you're running a classic fantasy HEROISM game, and the players start barking up the wrong tree, most gamemasters feel obligated to either subtly nudge them in the right direction or even use the magician's force and amend the backstory so that the direction the players chose IS the right direction. Eclipse Phase isn't necessarily about HEROISM. Horror is a perfectly fine outcome, too, and if the players screw up resulting in half the habitat (and even the players) dying in gruesome and horrific ways, that's FINE so long as it's ENTERTAINING for everyone involved and can be used to set up even more spooky darkness upon their resleeving.

Sounds like a good premise and as long as you're all having fun - you're doing it right. If someone loses an eye, probably not. (Should it not be entitled "The Origin of Species"?)