In Vol 2 we find out that it was Henry who discovered The Mind Flayer (or possibly created it) and decided to shape it into a large manifestation of the spiders that he was so obsessed with. Using his powers he was also able to control it as well.
We can also see now that Vecna was the one who possessed Will as the Mind Flayer. Him and Chrissy’s (and Vecna’s other victims) possessions are very similar to each other. You can see their eyes both rolling into the back of their heads here.
Will also confirms to Mike that it was Vecna who possessed him. He tells him that he could feel his emotions and that he knew what he was thinking. He basically has a direct connection to Vecna. This also makes him referring to the Mind Flayer as “he” make a lot more sense.
What I find interesting is that Vecna did not kill Will. Instead he kept him alive and used him as a personal spy for as long as he could. Although his plan was unsuccessful because Joyce, Nancy, and Jonathan managed to get the Mind Flayer out of him.
We know that the Mind Flayer ended up absorbing some of El’s powers at the end of s3, which is how he was able to see everyone in Hawkins in s4.
But before Will and before El, he must’ve had some way he was able to keep an eye on Hawkins so he could eventually execute his plans.
If he wanted to, he could’ve done his own dirty work instead but he decided to manipulate Will. I also find it interesting that when Will was first brought to the Upside Down by the Demogorgon (I believe was sent to Hawkins by Vecna), Will was kept alive unlike Barb who was also taken. Vecna could’ve killed him anytime he wanted to, but he didn’t and I believe there’s a reason.
I think Vecna has always had an eye on Will. Vecna can feel people’s emotions and he knows their thoughts, which is why he is able to use their traumas against them. Him and Will are both sensitive and they’re misunderstood by the people around them. They’re also treated as being different in comparison to others.
I believe Vecna could feel how similar they are which is why he chose Will specifically and kept him alive. He brought Will to the Upside Down, possibly with the intent of making him become evil or using him for a bigger plan. He just wanted someone like him to join his side, to become him as well.
Although, Hopper and Joyce ended up saving Will and cutting his plans short. But Vecna was still obsessed with Will which is why he continued to come after him as the Mind Flayer. He was so obsessed with him to the point that the Upside Down was stuck on the day that he disappeared, which is also the day Will arrived. Vecna is very particular about time and seems to hyper focus on the concept of time/clocks. So him stopping everything on that specific date is not accidental.
Now even though the Mind Flayer/Vecna is no longer inside Will, it has still somewhat attached itself to him and now he can sense whenever Vecna is around.
I truly believe that now that Will is back in Hawkins, Vecna will definitely come after him again. I don’t believe that he will come after him to kill him, but rather get him to join him. I believe that was his plan in the beginning initially when he took Will, because he wanted to craft him into another version of himself. And now that Will is closer once again, I don’t believe he will stop.
If anything, I also believe that Vecna attached himself to Will (or was trying) so that if something happened to him, he could easily transfer over to Will. Similar to how Harry was imprinted by Voldemort. As long as Will has that connection with him, Vecna can do whatever he wants with him. But knowing Will, I think he will try his hardest to fight against it. But what we don’t know for sure is if he’ll win.
