It might have already, but pretty much like ants aren't aware they make up a system that's greater than the sum its parts (i.e. an anthill), we might just not be aware of a higher-order intelligence we're part of.
Wouldn't it make sense that something on the level of a hydra or flatworm would develop prior to a rat-like entity, prior to a human level consciousness?
And it doesn't take consciousness or intelligence to manipulate intelligence; it just takes evolution and necessity, as is seen with plants, bacteria, fungi, and parasites.
The thing is, the constituents of such a system wouldn't necessarily recognise the higher-order system they're part of. An ant doesn't know it's part of an anthill.
Such a higher-order system wouldn't necessarily follow the same or even remotely similar evolutionary steps or patterns as the systems and structures that preceded it.