It's been bugging me but I remember watching an anime
and like in the ending, after the protagonist assumingly kills the villiann, the villian is unknowingly saved
and recruited by this group of people (they're in charge of the world or something) to be part of their organization to lead the world or something as he had potential for his extreme intellect (the villian was very intelligent)

i also remember a character being a lady, but in reality, that lady wasn't human but was a vessel for this man who was presumed dead, but was saved to be part of that group of people (like a higher order or something) so he assumes that new identity as the lady and plays a role as the boss or guide or whatever for the protagonists?

im sorry if it doesn't make sense, i just remember bits and pieces and it's driving me nuts I don't know what anime this is.

psycho pass

http://en.wikipedia.org/wiki/Psycho-Pass

I loved that one~♪

pretty sure that's the twist...

I'm not sure on this one. If I'm completely off the mark, I apologize. It sounds kinda similar to
Chaos;Head
but I am probably so far off the mark that I can't see it. It has some similarities but it would be in a different order.
http://en.wikipedia.org/wiki/Chaos;Head

Well, in any case. If this wasn't the one you were looking for I would recommend watching this one if you haven't. One of the few good psychological animes in my own opinion.

Good luck!

________________
Idk how many different mangas, manhuas or manhwas that I've read but it's more than 3000. More to come!
(Number of H-mangas and one-shots: unknown and not included)

Over 180 anime shows watched and there's a vast sea of shows to go.

J/K-drama's 50+ shows watched.
It's Mr to you!

Oh thanks you guys!

It's psychopass (I thought that originally but wanted to make sure)