I've listened to Ruvik's recordings and still have no idea what is going on. I get the STEM machine, I get Ruvik's motivations. But that's lore, not story or plot. What actually happens in the game makes zero sense. I've speculated and theorized in the spoiler thread and I've decided to give up because Mikami clearly is only interested in providing the vaguest backdrop and motivation as a literal handwave for why you go through variety of different environments that have no relation or reason for existing other than the lazy explanation of "they are physical manifestations of Ruvik's pain and anger" or some psychological babble like that. I mean Ruvik literally waves his hand and just teleports you to another level because there is no other logical transition from one level to the next.
The game feels like a videogame sketchbook of all of Mikami's ideas and inspirations that doesn't come together to make a satisfying game or story. If the DLC actually makes sense of anything, I will eat my face off.
Its all about connecting individual consciousness into a united realm. Ruvik partially controls that realm because his consciousness is the base-line due to the stem machine, hence his powers. ALL the locations in the game have been in Ruviks life at some point. He is emotionally attached to some, others are more filler (the city)