Stranger Things Season 2: What The Ending Really Means
5. Will Is Cured (But Might Still Be Connected)
After two seasons of being put through the ringer - with a side of The Exorcist liberally scattered all over him - Will Byers is seemingly cured. His infection - and connection to the Upside Down - had been kicked on another level by his contact in the Upside Down with the Mind Flayer, but his mother had burned out the infection, which broke the connection entirely.
But the infection wasn't Will's only connection to the Upside Down. Even after he coughed out the Demodog slug at the end of the first season he was struggling with terrifying visions that seemingly physically transported part of him to the Upside Down. As that all came before he met the Mind Flayer, the connection cannot be solely explained by that contact.
So even though he's over the escalated part of his "illness", there's no real guarantee that Will isn't still tied to the Upside Down. Perhaps the Gate being closed will stop it, but that's an assumption.
On top of that, there's no way Will isn't going to still be a pretty enticing target for the government when they get wind of everything that's happened.