Yeah the part which possessed Will in s2 and then Flayed and was in the proxy body in s3 is dead. But the Mind Flayer was in s4; he was the particles in the Russian gulag and then he possessed the Russian Demogorgon and demodogs. But that was just a part of him, yeah, idk what the rest of him was doing. Possibly in the Upside Down. But like, I guess the cursegates weren't open enough for him to seep through to Hawkins? But now they definitely are so we'll probably see him come into Hawkins in s5.