A "shadowy organization" refers to a secretive or mysterious group that operates in secret, hiding its true intentions or activities from public knowledge. Full definition
Nevertheless, Ethan and his associates (Jeremy Renner, Simon Pegg and Ving Rhames) decide they must act on their own to take down a dangerous, shadowy organization known as the Syndicate. (shepherdexpress.com)
Picture a land where nothing is what it seems, a network of shadowy organizations conspires to manipulate public opinion, and saying the wrong thing makes you a target. (edweek.org)
Once there, Lara crosses paths with her father's rival archaeologist, Mathias Vogel (Walton Goggins), who hopes to raid the cursed tomb of Queen Himiko, the Mother of Death, to bring back a piece of it to shadowy organization Trinity. (kibsreviews.blogspot.ru)