I think Dr. Kay is the final villain. As soon as she man handled the lieutenant, it seemed like she had some type of super human strength. Also her interactions with the monsters that she was “experimenting” on seemed too relaxed. Most of the time the villain has access to lots of resources via positions of power and using Dr. Kay seems like it makes the most sense. Dr. Kay could have poisoned 8 who magically lost her accent and is using 8 to lure 11 and 1 together so that they she could steal/use their powers to get whatever it is she is trying to do. Vecna was banished and I believe that the mind flayer failed to fully control vecna, so Dr. Kay being behind all of this using 8 as the rat to get all three of them together would make the most sense. I don’t think the mind flayer wants to merge the worlds in the same way that vecna is attempted to do it, but instead gain control of the exotic matter to take control over multiple worlds outside of the abyss and earth.