The Mind Flayer's hive mind allowed Henry Creel to become the version of Vecna that the audience will see in the fourth season of Stranger Things. Vecna built the Mind Flayer in the real world in order to circumvent Eleven's resistance, after she killed the Demogorgon and shut the gate on the Mind Flayer. Henry took control of the Mind Flayer particles and gave them form, turning the shadow monster into the Mind Flayer, a spider-like creature. The monster attacking, biting, and infecting its prey tracks with what happened in season 3 is different from what the Mind Flayer was doing to Will in season 2.
In season 1, viewers were given a glimpse of the Upside Down, Eleven's powers, and what the Demogorgon was, but that was only the beginning. Even though the Mind Flayer was removed from Will Byers, he is still connected to Vecna, even if the monster doesn't know it. When Vecna arrived in the Upside Down, he identified the Mind Flayer's particles/hive mind as the missing piece in his plan to gain ultimate power. The Mind Flayer and the Demogorgon in the first and second seasons of the show were meant to end, but they were stopped by Eleven. The Mind Flayer particles in the Upside Down connected him to this new world, even though his telepathy and telekinesis were useful.
Vecna was able to access people's minds across dimensions, killing them from the Upside Down and using their deaths to open new gates once he had Eleven's powers. Henry/One took control of the Mind Flayer and obtained all of his powers, thus becoming stronger and in control of the Upside Down. The Mind Flayer's second-in-command was thought to be Vecna. Various aspects of the Upside Down, Eleven's backstory, and even character motives have been shrouded in mystery for the past few seasons.
The Duffer Brothers noted several times that this would be the season of answers and reveals, and they weren't kidding.
Henry Creel, also known as One, created the Mind Flayer when he was in the Upside Down.
Vecna has been doing the Mind Flayer's bidding all along. The Mind Flayer was being turned into a spider-like creature to keep up with the monster's abilities. At the end of season 3 and the beginning of season 4, Eleven's powers were partially blocked because of that bite.
The pain Will Byers felt when he was attacked by a spider in the Creel house was similar to what he experienced when he was bitten by a black widow. The Mind Flayer joined the fight with his Demodogs and mass desiccation. He drew his own design when he was a kid at the Creel house. Black widow bite symptoms are the same length as Vecna's curse. He said that he broke free of his bonds and became the predator. Vecna acquires their consciousness and power when he kills someone.
Henry Creel had powers that allowed him to see into other people's minds and kill them.