The instant upgrade might also be explained by the fact that MC likes him and MC is the super intelligence created by the one who made the infinite horror world and fake outer and inner worlds. MC might have subconsciously given ML god tier luck.

It starts out with the abyss and sci-fi explanations for MC. Then in in the end it becomes like the matrix where everyone is actually in pods dreaming about the outer world and the infinite horror world. MC is actually a computer program and not a sci-fi monster, that to me is the major thing that feels like the author changed things halfway because there's such a gap.

The dream has infinite horror because the Scientist felt that it would give people more vitality and make the dream more realistic. Ok, sure author. People usually can't tell they are dreaming till they wake up. You can make countermeasures for people that wake up. If you really wanted to make the story, infinite horror is actually virtual reality, you could have set it so that people do make it out of the infinite horror but they never know that they are dreaming. Instead you write that S ranked people die from pollution, making a lot of things hopeless.

I get that the MC is supposed to be the final hope for a hopeless world, but the process to getting there should be more believable. In all honesty the Scientist could have soloed the story plot if he was the one that made everyone dream. The author just gave him negative IQ plot pills.

I will say there is a part where MC is absorbing power from the skill fragments, which are basically computer chips. This was probably the clue in that he's a program but there is so little world building or explanations about that ability you could chalk it up to other strange abilities that the MC has which will probably get explained later but it never does.