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.
Gates Becker and Joseph Sadaki Tokugawa are a corrupt police chief and a Corrupt Corporate Executive respectively who wish to push humankind into space to satisfy their desires for control and profit. With Gates as his hidden partner, Tokugawa created a Sex Slave operation where he had famous female celebrities cloned and used for pleasure by himself and the highest bidders. The two have anyone in their way assassinated and when Jonathan finds their headquarters, he realizes the extent of their evil: the two have been placing human beings in stasis and harvesting their organs while using cloning technology to regrow the organs for an endless supply.
Tony Redwood spends most of the game as a killer in a mask. When The Hero Jonathan Ingraham comes out of a 30 year stint in suspended animation, Redwood kills his former wife with a car bomb, and later in the game guns down another of his friends. In order to frame Jonathan, Redwood murders a captive scientist with Jonathan's gun, placing him under suspicion for the murder. To escape, he also installs a bomb in a civilian shop so the police have to choose between chasing Redwood or saving innocent lives. Redwood takes the adopted child of Jonathan's partner hostage later and puts the partner in the hospital. When another operative fails in her task to shut off his life support and shows signs of performing a Heel-Face Turn, Redwood murders her despite her being his own mother. When defeated, Redwood opts to throw himself to his death, laughing madly, solely to deny Jonathan the satisfaction of taking him in.
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.