They don’t really get into the “how” of it all with the protomolecule, far as I can remember.
Duarte has them going full out with their experiments on him, and it’s frankly never really clear that it’s mind controlling him at all.
It “shows him” how great it will be if all of civilization is one big hive mind, during his big “sleep” in Tiamats wrath, and when he wakes up in Leviathan Falls, he’s like “oh yeah, I just wasn’t thinking big enough!”
Frankly it fits his narcissistic tendencies pretty well, especially since he gets to be the one to make it happen.