According to Will in the season 3 episode, The Sauna Test, it appears while most of the Mind Flayer may still exist in the Upside Down and is probably running the show from there, another part of it still existed in Hawkins, as it (or at least, this part of it) was seeking to become more corporeal during the course of season 3.
WILL: I didn't think it was anything at first. I mean, I think I just
didn't want to believe it. The first time I felt it was at Day of the
MIKE: Power went out that night, too.-
WILL: And then I felt it again at the field near the Nelson farm the
next day. Then again yesterday outside Castle Byers.
MAX: What does it feel like?
WILL: It's almost like You know when you drop on a roller coaster? -
WILL: It's like everything inside your body is just sinking all at
once, but this is worse. Your body it goes cold and and you can't
breathe. I've felt it before, whenever he was close.
MAX: Whenever who was close?
WILL: The Mind Flayer.
Eleven: I closed the gate.
WILL: I know, but what if he never left? What if we locked him out
here with us? This is him. All of him. But, that day on the field, a
part of him attached itself to me. My mom got it out of me and Eleven
closed the gate. But the part that was still in me, what if it's still
in our world? In Hawkins.
MAX: I don't understand.The Demodogs died when El closed the gate. If
the brain dies, the body dies.
WILL: We can't take any chances. We need to assume the worst. The Mind
Flayer's back. Yeah. And if he is, he'd want to attach himself to
someone again. A new me.
LUCAS: A new host.
ELEVEN: How can you tell if someone is a host?
In addition there is even a brief conversation from the kids in another scene about "mixing chemicals" in order to make "a new substance" to explain away why the victims were eating certain things, but in all honesty, there isn't enough information to necessarily understand the Mind Flayer's full plan with the chemical-eating subplot.