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Nightmare Fuel: Mercenary Kings
Doctor Neil. Unlike Commander Baron, who was always treated as somewhat of a joke even by his own minions, Neil's depravity, madness and sheer sociopathy are all played dead seriously. From his Squicktastic plans for Bluebell, his depraved cloning experiments, and his downright terrifying One-Winged Angel form, Neil stands out as an incredibly dark villain for what was originally a fairly lighthearted game.
Until the Kings learned the truth, part of their mission was to save Neil and get him back to the mainland. If the Temple People hadn't told them of Neil's true intentions, nothing would have been able to stop him from unleashing the Ark on the world.
Special mention goes to right before the final battle, where to get to Neil's lair, you have to climb a literal mountain of mutilated, bloody Mandrake corpses.
Once you learn their true origins, The Prime Soldiers are both scary and depressing. Imagine going on a mission with your comrades, who are like a family to you, only to get brutally cut down one by one. Now imagine the enemy taking your corpses, pumping you full of a brainwashing Psycho Serum, then stuffing you in claustrophobic Powered Armor that forces you to try your hardest to kill your surviving friends.
Some of the enemies' death animations, despite being mostly played for laughs, can come off as a little disturbing, such as a Mandrake screaming before violently exploding.