"The Rebirth Initiative"
Ultimate Goal? Not world dominance, but a modified New World Order. Capture Supers, collectivize their powers and disperse this back into the genetic pool to give a mass reset to the entire world.
Scruples? Oddly, quite a few - while they will kill, hunt, wheel-n-deal; they ultimately want every formerly downtrodden individual to suddenly stand on equal footing with the rest of the world. Simultaneously wiping out cancer, plague, debt and nationalism.
Tropes: Magneto's (Movie) Brotherhood of Mutants, Fight Club -debt erasure, and "the gold-hearted mad scientist."
Means: Hiding out in individual countries with a combination of non-extradition clauses and few qualms with genetic engineering, they build charities, research centers, and political asylums. They will ALWAYS seem like "the good guys" compared to the PCs. For every bit of collateral damage, their media-relations folks will make the Heroes seem like pitiful fools hell bent on the destruction of "once safe and peaceful lands." Any attacks on their experimentation will be the sign of "environmentalist wackjobs."