In season 4, it was revealed that Vecna controls the Mind Flayer. But a new theory claims it is the other way around which would be a big twist in the final season.
Stranger Things has two big Upside Down villains: the Mind Flayer and Vecna. It seems that though Vecna is currently the biggest threat to Hawkins, the Mind Flayer could be potentially controlling him.
According to a fan theory on Reddit, if the Upside Down has been around for hundreds of years, then Henry Creel who was just around 30, arrived in the world of Mind Flayer when Eleven banished him. Though he became more powerful compared to his human form, it would seem that the Mind Flayer is way older and potentially more intimidating than Vecna. The user wrote this theory on Reddit.
"Dustin is heard saying in S4 that the upside-down has been around for “thousands, maybe millions of years.” This obviously does not coincide with Henry Creel, later Vecna, being only around 30 years old. Furthermore, when 011 sends 001 into the upside-down using her powers, we get a scene that reminds me a lot of Anakin in Star Wars. 001 is seen falling into a red abyss being hit with what seems to be fireballs of some sort. If Vecna created the upside-down, he obviously would not be getting hurt by it."
One fan agreed with this theory as he wrote,
Another user commented that Mind Flayer might have influenced Henry just like he did with Will Byers and Billy.
As of now, we don't know much about the connection between Vecna and Mind Flayer. Hopefully, it will be addressed in the final season of Stranger Things which will start filming next year.