This Cryptic Alliance is actually made up of many splinter groups that have on thing in common: they are genetists to some degree or another. The those with the lowest tech (III) are Mendelian in nature, and through advanced breeding techniques can add or remove mutations in relatively few generations. The most advanced can use retroviruses and metamorphosis viruses to alter adult organisms and are barely recognizable as human. They control the last of the working gengineering labs, and used them to the max. Of course most are less advanced, but almost all can be identified by the fact that none of their numbers have physical defects and even their livestock (if any) are very healthy and resistant to disease. Most try not to advertise themselves, as not to get waves of very defective people looking for a miracle cure. Those who do are either the very rare benevolent who can help them, or the variety who are looking for lab rats to work on. The different groups usually leave each other alone, mostly because the most advanced will get involved and try to stop any hostilities (this not just benevolence, some of them chose to spread the knowledge to acceptable less advanced groups). Of course this is a generalization that is broken from time to time. The Shapers fear (and are feared by) the Created. Both can seriously damage the other, and so violence is kept to a minimum. The only known battle between them ended with a deadland that won't be able support life for thousands of years (and the survivors could be counted on one hand).
PS The original source of inspiration was the octospiders in the Rama series by A.C. Clarke. Babylon 5, StarCraft, and now GURPS Bio-Tech have helped me to expand ideas for the Shapers.