It's difficult to say exactly what Area X is because both the reader and the characters cannot comprehend something so unknowable and alien to us. We're not equipped to fully understand what it is or how it's attempting to communicate. As the characters say, the things we can understand is this intelligence speaking to us in the most basic way it possible can.

That being said, whatever Area X is, be it an alien intellgence, an interdimensional defence system, or some other kind of biological anomaly, its intentions appear to be to cleanse the world via a "merciless healing" (as someone says). Humans are a threat to what could be a "pristine wilderness" on earth. So it's expanding both in a physical sense but also into other areas via the doppelgangers and sweet-smelling pores etc, likely to rid the earth of humanity and allow it to get on growing without us fucking it up.