I assume that will be explained. But I get the feeling he has been involved as soon as El opened the gate in s1. I think the demogorgon, the Mind Flayer, demodogs, etc were all weapons he was using to try to kill El, but since they all failed he finally decided to take matters into his own hands. Now he's opening more portals to make his connection to our dimension stronger so he's more difficult to defeat. If that's the case, Dustin's theory about him being the Mind Flayer's 5-star general is wrong. It makes more sense to me that Vecna would be the man behind it all since he has personal motives and is a better vessel for communicating that to audiences than a giant smoke monster thing.
However, the Upside Down likely existed long before Vecna arrived there, so maybe he is just a pawn of the Mind Flayer?
Time works in a different way in the upside-down it seems.
When the Hell fire club venture into it they were in the past..
A little bit of me is wondering if its linked to when they All first experienced the USD so maybe for Vecner it's another time zone.. Maybe it's a malstrom of zones all swirling but connected?
Also a theory of mine is..
Vecner has been waiting for El to save him, after all he certainly seemed good at the start and he only punished those who were hurting El in the first place. He is also a victim of what others have done to him by his captors..
That doesn't exonerated him from the recent deaths of course, assuming he's not himself trapped in a scoobie Doo way inside that form and El breaks him out pulling him out of the goo...
It's an 80s inspired show full of cunning tropes after all..