These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Nightmare Fuel: Wait until you see "the larger picture", a revelation with a scene that's even more shocking in the PC-98 version. Also, Ishida's murder, which borders on Gorn.
The Untwist: Jonathan thinks he's stumbled onto Tokugawa's illegal drug ring. In reality, the drugs are just the tip of iceberg. The real secret is that he's trafficking in humans to farm their organs.