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.
Epileptic Trees: A game like this inevitably has a number of these. Believe it or not, the game's manual itself actually goes into this. To directly quote from the manual..."When you really think about the power the TCTF wields it makes you wonder how the Syndicate has survived. There are a lot of theories: some say the World Coalition Government lets the Syndicate slide because they keep the underclass down. Others claim a connection between the Syndicate and the remnants of the countries erased by the World Coalition Government's land grab." To add to the fun, when you witness the events in the game and come across information in terminals, you will start wondering how much the theories above apply.
Goddamn Bats: Anyone with a machine pistol. It does low damage with a large spread and a high rate of fire, so you can't dodge it and don't want to use it either.
Good Bad Bugs: It is a tendency of the AI to grab any nearby guns for which they have ammo, reload, and then fire at you. Interrupt them by disarming them after the "reloading" step and you now have a fully loaded weapon that was empty two seconds ago.
Harsher in Hindsight: The manual says that the World Coalition Government's foundation came from a chain of events that started with money. Apparently, years of reckless spending and boom markets caused small countries to go bankrupt and superpowers teetering on the brink of collapse. Oh, and guess what? In real life, the world is currently going through a recession (some would call it the second Great Depression). Not quite to the level protrayed in this game, but this trope still applies.
Mass government surveillance of civilians, shockingly high levels of air pollution, bio-terrorism - a lot of aspects of this game's setting are just as relevant today as they were on the game's release.
He's Just Hiding: This game definitely has a number of characters who are given this treatment. A number of people think Barabas is not dead. Muro might still be alive. Griffin could be alive, especially if Konoko did not shoot him, but what if he survived getting shot? Fans think that Shinatama, despite everything that happens to her, still lives on - which is a possibility, because she could have created a duplicate of herself or transferred her soul to somewhere else. Mukade is very likely dead, thanks to having his neck crushed by Konoko's boot. However, fans have pointed out that Mukade was completely covered in armour, and that someone else could easily take on his name. A number of fans suspect that Dr. Hasegawa is not dead, and that he may be hiding...somewhere.
Magnificent Bastard: Muro, believe it or not. Think about it. He wiped out the Omniscient Council of Vagueness leading the Syndicate and became its sole leader (so the manual says). He had Chung the mole killed off and planted information on his corpse to lead Konoko in the wrong direction. Even when she figured it out and went in the right direction, he took off. He even managed to escape via the airport, even with her pursuing him. He had the Syndicate tear through TCTF headquarters just to snatch Shinatama. Even when Konoko eventually found out his plan, she could only disrupt it rather than stop him. That would be his plan to make the Atmospheric processors release poison instead of clean air, all so that he could give a Daodan Chrysalis to anyone who would swear loyalty to him.
Moral Event Horizon: Well, if the Syndicate goons gunning down scientists and civilians (shown on mission complete screens) were not considered this trope, the scene of Muro torturing Shinatama will be considered this. Some might think Griffin blowing up Shinatama or Konoko shooting Griffin qualify as this trope, but some might not think so.
Narm: The scene where Konoko yells "Muro! STOP!" is a bit narmy. Amanda Winn Lee seems to have a terrible habit of sounding unintentionally funny, especially when she is yelling.
That One Boss: Mukade, the master ninja. He has an invisibility device he can use whenever he wants, he teleports, he shoots homing energy balls, and he has the longest combo in the game, which can take off quite a bit of health if it all hits. Though you fight him on a rooftop, knocking him over the edge just makes him fly back up. There are more powerful bosses, but none more irritating.
Player Punch: Shinatama, especially after what she goes through with Muro and Griffin.