The perceived absence of the Mind Flayer seems to be present on everyones mind. However, the reason for this much like many previous questions that have been answered in the series may have been in front of us all along. Without further pause, let's get into why I believe the Mind Flayer is "gone", for now.

The Flayer has been present from what we have been able to see since at a minimum the end of Season 1. Dustin has postulated in Season 4 that the Upside Down itself has been around for thousands or millions of years leaving many to believe that the Flayer must be too. That said, I don't think so. What follows is why.

The connection to the Flayer and Eleven was more than established in Season 3. When Billy was controlled by the Flayer it stated that it had been working, building, and suffering for her. Such a strong connection for what? Shutting the gate? Possibly, but I believe there's more. More than Eleven knows about their connection perhaps even their "destiny".

In Season 4 we now have the luxury of seeing before the events of Season 1. We now know she opened the gate on another occasion 4 years previous in 1979 not 1983. Why is this important? Because if the Flayer was around then why did it not know of that opening in Season 3 during the Eleven entering Billys mind scene? The Flayer specifically showed Eleven the 1983 opening. Why?

That is because IMO the Flayer at least as we know it was born the day Elevens powers became so great that the Upside Down birthed an equal and opposite power to match hers. What date is that? November 6th 1983! It explains why the Mind Flayer is "gone" now. Think back to Season 3 Elevens powers faded as the Flayers power over Billy faded. When she lost her powers so did the Flayer and now it is a shell of its former power just like Eleven. Now the Flayer has attached what remains of itself to One/Vecna to lure Eleven into regaining her/it's power.

What does this mean for Stranger Things? IMO, What we can expect is an awakening of the Flayer as Eleven regains her powers in Season 4 part 2. Another element to watch for is like an Endgame/Doctor Strange type plot. Time travel has now been hinted at going back to Season 3 with "Back to the Future", Hop's letter to Eleven, Elevens opening monolog in Season 4 and the fact that the Upside Down is "stuck" in 1983. To defeat both Vecna and the Flayer will require Elevens realization to the above connection to the Flayer and for her to "kill herself" in order for the Flayer to "die" at the end of Season 4.

This is where things could get even more weird for series and the "time travel" could come into play. IMO that is why the Flayer preserved a copy of that date In 1983 so that the Flayer could be reborn in a recreation of that day in the Upside Down and Eleven with it . However, that would leave her "trapped" on that side in the possession of the Flayer. However, I believe that won't come until the 5th and final season but will be teased after the credit scene when Eleven is seen "trapped" in a "loop" of all the events in S1-4 just like her "Mama". This loop is also hinted at with the Never Ending Story in Season 3.

Like the Flayer told her in Season 3 all of it was built for her!

For supporting evidence of the "death" of Eleven can be found Episode 1 of Season 4 with the D&D dice rolls: The first roll was 11. I think this foreshadows that 11 will fail this season and will at least appear to be "dead" likely at the hands of the Flayer.

For the second roll, it was a 20. I was personally thinking that after watching everything that follows that it is foreshadowing the potential convergence of all three test subjects we know now to still exist 11 8 1=20. Likely this takes place next season after One/Vecna realizes he's been played by the Flayer and reaches out psychically to 8 and they together "resurrect/release" 11 becoming the 20 roll at last defeating the Flayer for good. Just a theory... A fan theory. 😉