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I don't think any mundane biological weapons would work on them being that they are supernatural. A magical plague however......

Perhaps as a normal standard in developing new deseases, it happened by accident. One of the original research crewmen had suffered a serious injury resulting from an meteorite impact to their vessel.

A piece of chemically active material (from the void of space) logded itself deeply into one of the rogue promethians. As a natural reaction, the promethean attempted to phase himself and eliminate the object. It just so happens that the object phases with him!

Desperate, the other prometheans on-board took their wounded comrade to the medical facility. There, they used nanites (while he's un-phased) to seekout and destroy the logded object (as their natural phase powers and psychic powers were of no use). Upon reaching the object the nanites did indeed "eat" away the substance...but nearing the end of their meal, the promethean awoke (from his heavy psychic sedation) and unconsciously phased...phasing the now chemically polluted nanites, and producing a deadly new type of pathogen.

Originally the logded "substance" was naturally highly resistance to psychic influence. It was actually a piece a ship (long since gone) that was constructed completely out of this material in order to combat a race of psychically endowed beings (your pick). While this "meteorite" journeyed through space, certain other "qualities" where inherited.

Tid-bits?

The nanites were already considered an "intelligent" programmed device. Now...altered...they have their own wicked spirit.

They use the bodies of prometheans and psychics (as they too can be "infected"...just not destroyed) as transportation. Puppeting the body after numbing the mind.

Side-effect of infection, HIGHLY (almost immune) to psychic powers...all type (including telekinesis and remote viewing). The eyes of the infected (especially prometheans) are glossed over with a metallic hue. Any object to hit the promethean while phased, will do X2 damage and act as if he weren't phased at all (although still seeming phased). The only reason the now-controlled promethean will phase is to release the deadly virus (as they cannot be released any other way).

*Yes, this means if they infect a psychic...either they just plan on gathering intelligence and using it an attack "vehicle", or they must find phase technology inorder to release itself.

The Nanites can access 75% of the psychics abilities. It takes approximately 15 minutes to kill a promethean (if desired).

Thanks all. Now that my imaginative energies have been expended, my players will have to settle with another "defeat the bogie-man and save the princess" senerio...