4. Reapers (Mass Effect trilogy)
So, it turns out that they actually don't want to doom organics into extinction. If they did, they wouldn't be going back to eliminate civilizations over and over again. The Reapers just want to harvest all the organics to prevent an "inevitable" war with synthetics that will extinct all organics. So, yes they will kill everyone to save the organic species as a whole. Tough love.
You do have a choice to rectify this with the choices presented in the end and that's a whole different debate on it's own.