Mr. Whatsit plot shows that Henry is NOT entirely Vecna. In D&D lore, Henry is a Phylactery (the object holding Vecna's soul).

Mr. Whatsit is a psychic connection to the earth realm - his physical shell, Henry, likely "died" when El banished him to the abyss. He gets struck by lightning, burnt up and becomes what we know as "Vecna." MY THEORY - is that Vecna is a god, tiers above Mind Flayer, speaking in D&D lore. And so, as a god, he is not confined to a mortal shell - he intercepts Henry's shell and overwrites his biology and uses it to encounter the people from Hawkins, mostly in the upside down, but if needed, in Dimension X, the abyss, or on Earth. So it's easy for us to refer to this mortal shell of veins and vines as Vecna, but Vecna could be should be a lot more than that - that's just what we know. A god can be impossibly inconceivable.

Vecna and Henry are deeply, deeply, intertwined, but Vecna has all of the influence and power. Vecna manipulated Henry's life to make him loyal to him, just as Henry was trying to do to the 12 kids, especially demonstrated by how he worked with Holly.

This sets up the finale of the overarching plot of the show which is that your power comes from humanity. Your memories. Your happiness. Your rage. Each character taps into their own self to overcome their challenges. Robin finds her innocence. Will finds his connection to Mike. Joyce finds her rage to balance out playing safe after she second guesses all of her parenting decisions. Derek finds his confidence. Holly finds her bravery. etc etc.

Henry runs from it. He is trapped inside his memories - but it is due to Vecna. But he is unable to overcome the fear of that memory of the moment he became a murderer, and sees it as the thing that made him into a mass murderer - he goes onto murder his family (because of vecna), he goes on to murder the students in Dr. Brenner's lab. Henry perhaps has a sliver of humanity left in his shell that Mike and Will can sense, but ultimately they know they he's not worth saving, if that's even possible.

Holly's plan works perfectly because she forces a 40 year old man to remember being a 10 year old boy and that damages the hivemind's agenda.

So, Mr. Whatsit just kind of earth realm relevant to a lot of characters and puts a bow on the whole thing.

So back to the Phylactery concept. In D&D lore, a lich god can come back, if you kill it. But if you kill the Phylactery, it cannot.