There are a lot of questions about Misery's actions in the game. Given her powers, she could curbstomp Quote early on, or teleport him to the Labyrinth, or off the edge of the island— yet every time she appears, she seems to cause a fight with another boss rather than fighting you herself. This would seem like Sorting Algorithm of Evil, but the true ending makes her actions make sense; she was half-assing her attempts to kill you, which were presumably ordered by The Doctor. She is bound to obey whomever wears the Crown, but she knows that you are the best shot at destroying the Crown, and eventually Ballos, and so she allows you to get closer to your objective. She even sends you to the Labyrinth, where the Core is kept, and sends Balrog with you so that you can make it through the Boulder Chamber!
Cave Story: At first, I thought the music of the Plantation stage was a bit out of place, as it's a very jaunty tune for the place where the Mimigas are being forced to grow the very flowers that would transform them into monsters. Then, after a pointer from another troper, I realized: Plantation seems pretty pleasant at first glance. It's a Breather Level, and one of the brighter caverns in the game (and if you're on track to unlocking the True Final Boss, it's where you get reunited with Curly Brace). The nasty bit about the Mimigas farming the instruments of their own destruction is something that only becomes apparent after some thought (or obtaining the Mimiga mask). The music mirrors this: It starts off sounding quite upbeat and determined, and loops through a complete melody twice—then in the third loop (1:38 into the song) a counter-melody begins playing and the whole song goes confusing and dissonant. (None of the other tracks in the game feature a fakeout along those lines.) In other words, the level is Fridge Horror, and the music matches that. -Meta Four
What really had me thinking was that the Plantation theme and the main theme used in the title screen are identical. It's at this point of the game when you finally realize exactly what you're supposed to do, and how you're going to do it. When you began, you only had a faint idea of what to do, and everything felt unexplained. But now you've taken a huge responsibility, and after this is the point where things become Nintendo Hard. It's also a bit of a musical Title Drop.
I'd been wondering why Curly hadn't tried to help you during the fight with the Doctor. I mean, she said she wanted to get back at him for kidnapping the Colons, so I thought it'd make sense for her to show up and help out. Even more confusing was her appearance in the Sacred Grounds. But then I remembered what she'd said after memory was restored: She and Quote had been sent to destroy the Demon Crown. She must have figured Jenka might know something about it, and so went to see her. Jenka would've explained the whole 'Ballos' thing, and Curly, armed with this knowledge, would have gone to destroy Ballos, and thus, the Demon Crown! -phazonfarmer
Everyone who's played the game will tell you that Moonsong is one of the greatest pieces in the game. When asked, they will invariably respond "Because that's when you finally get outside!" It wasn't until recently that I realized that it's more than that: When playing the game for the first time, by this point in the game you've lost four of your friends to the actions of the Doctor. Walking through the emptied Mimiga Village adds to this, as you can safely assume that that same man has abducted all of its inhabitants. The only indicator that anyone escaped is a one-sentence message that tells you to head to the Egg Corridor. When you go there, you have to fight your way through a large number of powerful enemies, and when you get to the end, you'll be ready to tear something apart. Then Kazuma shows up, explains what happened, and offers you a chance to cut your losses and leave the island. When you select 'No' and step outside to continue pursuing the Doctor, the beauty of the clouds rolling by, combined with the music, will dispel any rage the player had been feeling, and replace it with Heroic Resolve. That moment contains so much emotion that goes unnoticed: Sadness, anger, but with an undercurrent of hope. The music understands this and simply adds to it. The fact that you're outside is more like a dose of Fanservice. -phazonfarmer
Reading this really made me want to see this scene animated. With Quote deciding to go with Kozuma, but upon stepping outside feeling the wind on his face and seeing the clouds rush by and the moon shining bright he reflects on the previous deaths and bad moments (meanwhile Moonsong builds up). Kozuma asks "Are you ready?" And Quote just starts climbing up the side without answering back.
People remark about how the Blade is ridiculously overpowered if you spam it at point-blank range (as it works by the One Bullet at a Time mechanic, the closer you are to your target, the quicker the blade will hit and disappear and thus the quicker you can fire off another one). Think about it. The game isn't broken by this, it is rewarding you for using the Blade as what it is - a melee weapon. - K.o.R
In the Nicalis translation, Balrog calls Jenka "auntie". It might seem like he's just teasing her about her age, but in the harder ending, Jenka turns out to have a brother who would be very capable indeed of creating Balrog. -unclghost
This may provide a likely explanation for why he too was bound to the crown.
There's only one Mimiga colored a different color than all the rest. Her name? Chaco. Pronounced as in 'chocolate'.
When you are making your way out of the Labyrinth, you can talk to a hurt Prof. Booster who is now trapped as well. He gives you the Booster v0.8 to escape and presumably dies in there. Alternatively, you can exit the area without talking to him, where he lives and gives you a better jetpack later. This makes sense, as you left him with the original jetpack, giving him a way to escape the Labyrinth and recover from his wounds.
When you bump into Professor Booster in the true path you can take the teleporter to a new location. That location just happens to be the broken teleporter just below where he fell. The implication is that he fixed it and used it to get back. He didn't use the Booster 0.8 to escape. A much more likely explanation was that since he didn't bump into Quote, his determination to make things go right kept him alive. Meeting Quote there had the unfortunate side effect of letting him accept his death.
Could be both. Humans probably can't jump and survive falls the way Quote and Curly can, so he probably needed the Booster 0.8 just to get safely down to the teleporter.
Considering he'd already just fell a huge distance, I don't think that's it. It's likely that Booster used the...well, Booster for spare parts to fix the teleporter, make it back to Arthur's house and heal himself. Thing is, in the path to the bad ending, with player getting trapped down in the pit, Booster figured out that you needed to get out more than he did so you could save the day, thus he was unable to heal his own wounds. -InfinityAlex
Alright, here's a huge one. Curly Brace rides on top of Quote's shoulder for the end of the game. The curly brace keys are above the Quote key on the keyboard.
As amusing as this is, it's not the case on a Japanese keyboard, in which the quote key is shift+2 for some reason.
So, why does the Jenka song play in the first room of the labyrinth? Jenka was the one that built the labyrinth in the first place.
Why does Santa have a deathtrap in his house? Well, consider why spikes would be there in the first place. Pretty much everything red in the game ties in some way to Ballos's runaway power - the red flowers are caused by him, the Demon Crown he created regenerates as long as he's alive, and the Last Cave that's roughly adjacent to the Sanctuary is filled with red enemies and pools of damaging red lava. The spikes are also red. All the spikes in the game were also generated by Ballos's magic, appearing wherever it's least convenient. It's almost a miracle Santa has the only house that's been breached by them.
How many Mimiga children is Curly Brace raising? Four. On the balcony, how many frenzied Mimigas are there? Four...
Some of the sidequests can invoke this depending on the ending that is being invoked, especially the Normal ending whilst holding Mr. Little inside your inventory. indirectly, you may have killed his entire family by destroying the Undead Core and causing the island to plummet to the Earth, he still says "...Aren't you forgetting something?!"
The red flowers in Arthur's basement. The Red Demon has suspiciously rabbit-like appendages on its head...
The flowers also explain the enraged mimiga guarding the Dragon egg in the egg corridor. In the Nicalis translation, before the fight, the enraged Mimiga will say that "Nobody can touch Masters eggs", and, after defeating him, in the unnofficial and official translation, you learn his name was Igor. Which means that, in the end, Kazuma fed an innocent Mimiga red flowers to use as a body-guard.
It seems far more likely that this Mimiga is a survivor of the events which happened when the soldiers from the surface ascended to the island to stop the previous Master of the Demon Crown— The facility is far too high-tech to originate on the island, and breeding very powerful dragons would seem to tie quite well into the idea of world domination...
Visiting Jack around the time you go to Sand Zone nets you some exposition, revealing that Arthur actually banished the Red Demon from Mimiga Village before The Doctor even came along, thus earning his title of "Hero".
Which would imply that Arthur was using the red flowers. Now, consider that King's eyes are the same color that Toroko's were after eating a red flower.
Well, Word of God does say that King did eat red flowers... Except he cooked them first, meaning there is a way to safely consume them, albeit at the cost of reducing their effect.
When you're in the Plantation, you can find Sue, Jack and Mahin in jail. Later, when you're sent there, two are accounted for... Where did Jack go???
He could very well be in one of the cages in the room where you fight the Doctor.
In The Sand Zone, after coming back with the last dog, all the other dogs are gone and Balrog's gloating about having the keys... Did he start killing her dogs to make her give him the keys? It helps that you never see them again for the rest of the game.
It doesn't help that the area right before Ballos has a dog that says to "please kill my master", and then disappears like a ghost.
In the Labyrinth, you go along with Curly and obliterate everything in your path at one point. In these areas, there are plenty of eggs which seem to be guarded by the armored cockroach creatures. Since the creatures are there to protect the core, it's implied that these eggs contain more creatures/protectors. You destroy them all (possibly not all, but certainly alot of them) while fighting through this area, so that means you just destroyed their upcoming generation. This doesn't seem that bad since most of the creatures are hostile; but as proved by the Shop and Clinic in the Labyrinth, there are plenty of them that are thinking creatures with feelings. You just killed those too. Made worse when possibly all of them are intelligent creatures, considering that they're just doing a job.
In the Bittersweet Ending, the island falls out of the sky, killing anyone on in on impact. Or did it? Ballos is a man of supernatural power, and let it run rampant in order to free himself from royal torture. It's possible they protected him from the impact. Not a good thought considering his own sister, the only one who could match him (besides you, of course), used up the last of her power to subdue him and likely perished on impact.