First thing I noticed was that Cinder's group is terribly well funded for such a small team, more so than their professional terrorist allies, the White Fang. Furthermore, she is clearly a well-trained spy, infiltrator, and assassin who appears to somehow have access to cutting-edge Atlas military hardware, including a top secret prototype mech. No one could get ahold of that kind of gear unless they were very high ranking within the Atlas hierarchy.
I've seen a suggestion that Ironwood might be in on it. While that would explain her access to hardware, it doesn't seem to fit. Remember that Cinder hacked his phone and was genuinely surprised to learn about Penny. His part is that of the well-intentioned but misguided good guy who ends up accidentally doing more harm than good. When it blows up in his face, he will apologize to Ozpin and fall into line.
If Cinder is the Queen, who is the King? Ironwood is prideful, but not ambitious. Whom do we know of from Atlas who has the wealth to fund a small army, the connections to supply them with Atlas hardware, and a combination of ambition and ruthlessness to see an operation of this scope played out? I believe that our elusive man behind the curtain is none other than Daddy-dearest to Weiss and Winter.
I suggest that he intends to undo the old man's gifts and take them back from the maidens. With such power, he could rule all the kingdoms.