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- It Was His Sled: The Big Bad is sentient mitochondria that wants replace humans at the top of the food chain. Adaptation Displacement will do that.
- Some Anvils Need to Be Dropped: Even with the whole "transplanted organs will make a host for an ancient evil" thing in the story, Sena still tries to show organ transplantation is a beneficial practice.
- Squick: Anything Eve does, like creating a body, or raping Toshiaki, or raping Mariko.
- Special Effects Failure: The fire is even awfully designed for its day, not appearing anything like fire or flames actually look. Even contemporary music videos were better at depicting CGI fire at the time.
The First Game
- Adaptation Displacement: You mean there was a movie? And - gasp - a book?
- It probably didn't help that their international releases were delayed several years, and weren't around for long once they were. The novel was actually not published in English until 2007, and it's rather rare in a lot of North America.
- Awesome Music: Primal Eyes, full stop. Also, Kyrie.
- Disappointing Last Level: Day 6 starts with a multi-stage boss, which, while impressive, is no match for the Suspicious Video Game Generosity that immediately precedes it. Defeating it leads to a chase through the maze-like interior of a ship which, while certainly tense, requires no wrong moves whatsoever through the unmarked tunnels, with the slightest mistake or deviation being punished with a One-Hit KO. And failing to realize one has to activate the boiler along the way just makes the chase Unwinnable. Also, you'll have to re-fight the final boss and sit through unskippable cutscenes and dialogue first each time you try.
- Game Breaker: The Super Toolkit available in New Game+ (aka "EX Mode"), although the upgrades are still limited by the attribute "donor" items and the upgrade capacity of the target. And whether you collected all of the Rare Trading Cards for it; miss a few and you'll be awarded a lesser version that destroys donor items.
- You play your cards right, you can put together a pretty cheesed up weapon on your first playthrough. How about a handgun that fires two salvos of flaming shotgun rounds? Yes please!
- In an LP, the player managed to put together a gun that fired grenades full of acid and liquid nitrogen in shotgun spray.
- Upgrading a gun's ammo capacity and range to high enough levels can let you attack monsters from any spot on the battlefield (unless they fly/dig off screen) and never having to reload.
- Adding the shotgun effect to regular rifles or handguns makes the things effectively fire flechettes for full effect in a cone, neatly breaking the rate of fire problem noted in Awesome, but Impractical.
- Guns that have the "Enter 2 (or 3) Commands" effect can offset the rate of fire problem described above, allowing you to shoot multiple times but have the attack power be based on a single bullet per shot instead.
- Even moreso, you can and do use a Power as a command, meaning that that mod can have you fire off multiple powers, possibly mixed with gunfire.
- Powering up your armor enough can let you be completely immune to damage from almost every enemy attack and you will need it when tackling the higher levels of the Chrysler Building.
- You can also modify your armor to make you immune to every single status ailment in the entire game, with the exception of Defense Down.
- Most Annoying Sound: The crunching noise weapons with frost effect make.
- Paranoia Fuel: You have a mitochondrion in every cell of your body. They're the chemical engines of life, and without them you'd die in minutes. And they're of such alien origin that they even have their own DNA, rather than being coded in the nuclear genome that describes every other aspect of your phenotype. What if one day they decide they hate you, and they should revolt?
- Squick: Hans provided scientifically altered sperm to Eve. How he donated it is the question...
- Tear Jerker: The entirety of "Someone Calls to Me, Someone Looks for Me".
- That One Boss: Fighting Maya isn't terribly difficult until you start to whittle her HP down. She can perform several kicks that you can't avoid at all and she can also do a charged up flying tackle that is both unavoidable AND doubles as an HP to 1 move. What's even worse is due to the game employing Collision Damage, if you get stuck on top of her after her tackle attack ends, you can take additional damage and possibly die. When Maya has her helpers summoned, attacking her has a second helper appear that heals her for 1000 HP and additional healing raises it by an extra 1000 points (And good luck figuring that one out). You NEED Auto Heal and plenty of Medicine 3 and 4 to be able to survive the fight since your turns will never come up fast enough to let you heal yourself manually.
- The Spider boss is a pain in the neck. It will root the player in place with a hard-to-dodge web attack that paralyzes them and deals damage over time, and actually shooting it means getting in range of its powerful melee attack. And it's followed and preceded by a looooot of unskippable dialogue and a Kaizo Trap that the game does a very bad job of explaining how to escape .
- The Woobie: From what we learn of her, Melissa Pierce. She was an Ill Girl since her youth and all the way up to adulthood was hooked up on medication. Despite that, she struggled to become an opera singer and had to share her part with someone else. And then on her opening night, she was taken over by Eve thanks to a kidney transplant supplied by Maya back in her youth as well as further medication by Klamp that would make her body even more susceptible to Mitochondria Possession.
- Unwinnable by Insanity: After defeating the Ultimate Being, it starts to chase after you and gradually picks up speed. When you reach the boiler room, Aya notes that she should overload it so that the ship explodes and kills the creature. However, you can actually skip the self destruct sequence and keep going. If you choose not to blow up the ship, the creature will move so fast that it will catch up and kill you instantly no matter what you do. Only by rigging the ship to explode will the creature move at a pace that keeps you on your toes yet still give you a chance to escape.
- Visual Effects of Awesome: The graphics during the mutations were really ahead of their time, and still hold up today.