I'm warning you, this post will be extremely long and will contain many spoilers.

Let's start by reviewing the series' premise, specifically Henry Creel's monologue. I quote: At first, I thought you sent me to my death, to purgatory, but then I realized it was a world that humans hadn't managed to corrupt. I became an explorer, and one day, I discovered the most extraordinary thing of all, the thing that could change everything. It gave me the opportunity to realize my potential, to transcend the boundaries of human form, to become the predator I was born to be. After this, we see Henry transform a living particle storm into the Mind Flayer. Many mistakenly believe Henry created these particles, but no, the Mind Flayer has always existed in this dimension. To summarize, Henry found the Shadow Monster and shaped it, giving it purpose and motivation. I'd also like to point out that Vecna ​​didn't explicitly say he controlled the Shadow. When he said he transcended the human body, he meant he tapped into the hive mind and was able to remotely control the Demogorgons, Demobats, and Tentacles. Their relationship with the Shadow Monster is unknown, but it's safe to say he partially controlled the Meat Flayer.

Now consider the plot of the play "First Shadow," which is also canon. Here, we're clearly told that Geri wasn't always a sadistic, human-hating psychopath; he was corrupted by the Shadow Monster, and the particles infected Henry's blood, giving him abilities. Henry was also shown to have a girlfriend, Patty, whom he tried to protect from Brenner and the Mind Flayer. However, it's not entirely clear whether the Shadow completely possessed Henry or whether Henry was able to resist it (which is unlikely). The play's conclusion: the Mind Flayer is the rightful ruler of Dimension X and the Upside Down, Vecna ​​his victim, whom he corrupted and made his avatar.

Now let's examine the plot of the VR game, which is also canon. It's relatively simple: we're shown that the Shadow Monster and Henry work together, occupying equal positions in the hierarchy. The Mind Flayer gave Gary powers and an army, and Henry became his general. The Mind Flayer needs to take over the world, Henry needs revenge on Jane, and they help each other.

The game's conclusion: Henry and the Flayer are co-rulers of Dimension X and the Upside Down, the Mind Flayer is the source of power and energy, and Henry is a strategist and genius.

Now the final conclusion: who is the real main villain? The answer is both of them. If you kill the Shadow Monster, all the demogorgons, tentacles, demobats, the entire Upside Down, Dimension X, and Vecna ​​will die. But if you kill Vecna ​​and close the portal, the Mind Flayer will no longer be able to enter our world, leaving it without a counterfeit.