The Shadow Initiative was assembled by Camp Hammond's base manager Henry Peter Gyrich out of Initiative recruits. They served as a black ops unit for Gyrich and the subsequent Initiative commanders until Norman Osborn and the Taskmaster assumed control of the Initiative. They reworked the Shadow Initiative into an army of cannon fodder, otherwise useless recruits to be thrown en masse at an enemy, regardless of the consequences.
Other members unrelated to the X-Men include Bengal, Trauma, the Scarlet Spiders, and Komodo.