How could the fake Zilch leave Kanai Ward in Chapter 0 without running into his weakness to sunlight? Makoto probably pulled some strings so the Amaterasu Express' windows would have UV filtration. So as long as he didn't leave the train he'd be fine. If he was waiting on the train and killed the real Zilch after he boarded, he wouldn't need to. And he had access to the Main Control Room, which didn't have windows to begin with.
Why did the developers choose to have the fake Zilch kill the other detectives by burning them rather than use another method such as stabbing? Besides the fact that burning allowed for the twist that the fake Zilch could fake his death by using Aphex's charred corpse, stabbing them would have also created blood, more specifically, red blood, which would have ruined the much later twist that all the residents of Kanai Ward are homunculi and thus have pink blood.
In-universe, why would the fake Zilch choose to burn the other detectives alive? Well, his like is listed as "Destroying nature". What's a well-known way to destroy nature? Forest fires. It's probably his preferred method of killing.
Makoto mentions that he doesn’t have a license when he’s about to drive Yuma to Amaterasu HQ in Chapter Four and this makes perfect sense for one big reason. Assuming that Kanai Ward natives can even get licenses in the first place with their isolation, Makoto’s face would be broadcasted to an outside organization which would create an information leak about who he’s related to and raise all sorts of questions he would not want to answer and ruin his manipulation of the WDO.
How did a total space cadet like Fubuki manage to easily pass the tests and training to quickly become a certified Master Detective? By rewinding time until she achieved favorable results.
None of the Master Detectives Yuma meets have a Forte that is particularly useful in a fight - at best, some have an ability that can make avoiding or escaping a fight easier. This reinforces the idea of working together with and relying on others when your own abilities won't cut it.
Kanai Tower looks like an umbrella, albeit without the cloth portion. Makoto in turn is a shield of Kanai Ward's residents from the rest of the world.
Why is Halara so trusting of only the WDO and Yakou Furio throughout their assignment despite only trusting the words and requests of those who pay them? Because the WDO already paid for them, and practically already did it to Halara's required estimate what with them being an incredibly wealthy organization, so they have every reason to trust their employers.
Given how willing Yomi was to kill the previous CEO of Amatarasu, it seems odd that Makoto seems to have gone unscathed for three years even if one accounts for his high security and cautiousness with Yomi. But then one realizes he may well have been targeted at points, his body then left in a hidden location or dumped somewhere, only to come back to life later given he is a perfect homunculus, and perhaps play up his seeming invincibility to make Yomi hesitate to try again.
Even beyond the issue of corruption in Kanai Ward, and the fact that the Mystery Labyrinth almost always tells you right away if you get something wrong (or does so with a roundabout method), the Mystery Labyrinth is a far more useful tool for solving mysteries for one key reason: The difference between solving and proving a case. In the Mystery Labyrinth, you only really need to do the former, and the progress gained in the labyrinth proves all for you. In the main universe, you have to do both. As Halara mentions, despite their incredible detective skill and relative ease in solving the Nail Man Murders (In comparison to Yuma, who struggles to figure it all out until reaching the Mystery Labyrinth), clients rarely believe them in regards to Post-Cognition. Using the Mystery Labyrinth allows the user to skip that step (Especially if they have someone like Shinigami guiding them, who can possess the culprit and have them admit to the whole thing), providing another reason for why detectives might've used it in the past even if they weren't going somewhere like Kanai Ward where the 'Law Enforcement' was incredibly corrupt.
It seems rather odd that no one in the NDA mentions recognizing Yuma's face or hearing about his Forte, even though a trainee within an organization like the WDO would be all the agents would be talking about. Halara and the others even knew Vivia and that man has no desire to interact with anyone, trying to stay out of everyone's way. So why did they not recognize anything physical about "Yuma" or his "introduction" to the WDO? Because he was actually the true Number One, who intentionally avoids being seen by others, so of course no one would recognize anything about him.
It's notable that Yakou getting Halara and Vivia away from him in Chapter 4 is a key plot point. In fact, it's the very reason their presence in the research lab comes as a surprise. They never meet Huesca because they come back after he's dead, along with the chief. So what was that for? He knew the two of them were too competent, and if they observed his crime happening in motion, they'd immediately notice something's wrong.
Why is Yuma Number One when he seems younger than most of the other Master Detectives? It likely comes down to operational experience. Zange seems to prefer cases that peak his excitement. Zilch (at least going by what his assassin says) only does cases outside civilization. Aphex is mistrusting of people, which doesn't exactly get you a lot of clients. Melami, nice as she is, limits herself to cases where she has no trouble donning a victim's clothes to channel them. Pucci seems to focus mostly on business cases. Halara will only take cases where they're paid large sums of money. Desuhiko, disliking blood, prefers infiltration and undercover work. And then there's Fubuki and Vivia, who are ditzy and lazy respectively and probably don't take on that many cases. But Yuma can be seen taking on any case at any time, sometimes even in the middle of investigating another case. He even notes to Shinigami (while still having his memories as Number One) that he wants to make as many people happy as possible by solving mysteries, which means he's likely taken on cases no other Master Detective will. He's probably solved more cases on his own than the other Master Detectives we've seen put together.
Yuma's narration of the opening to each chapter can come across as wooden and stiff, which can be weird considering how emotional he normally is in-game. But then you realize it's most likely Number One, aka the man who discarded all emotions for a perfect solution, narrating and suddenly it makes more sense.
The consistencies between the personalities of Yuma and Makoto coincide with the fact that Makoto is Number One's clone and Yuma is said Number One. This includes their extremism (Yuma erased his memories, made a pact with a death god, and snuck into Kanai Ward by swapping with the real Yuma; Makoto did everything in his capability to keep Kanai Ward safe from the Unified Government no matter what, which ends up turning him amoral and willing to do anything to protect the homunculi within it), their stoicism as a result of Number One's philosophy of discarding emotions (Number One is shown to be stoic in Shinigami's flashback; Makoto also presents a stoic demeanor throughout the whole game), and their intellect which coincides with that extremism due to them both trying to find a "perfect solution" to their problems (Number One's overarching scheme was intended for him to enter Kanai Ward and confront Makoto; meanwhile, Makoto is an active Manipulative Bastard who takes advantage of everyone and everything around him, with the intention of providing Kanai Ward's homunculi a safe place to live).
It seems rather odd for Zilch not to bring any animals with him on the train when his Forte revolves around them. But who's to say he didn't? He could've brought along plenty of cute little animal pals, which becomes horrifying when one remembers that the assassin impersonating him loves destroying nature and killing animals...
Since there's no doubt that they have souls, otherwise Shinigami wouldn't have anything to reap, what happens to the homunculi when they revive as zombies? Do they lack souls entirely or is a new soul created in/bestowed to the mindless, shambling monstrosity? And what about those who died through conventional means? Do they have a first soul going on to an afterlife or is the same soul unable to leave its prison of defective flesh? Might Yuma have been doing the culprits a favor by killing them?
While the main story never calls attention to it, the Gumshoe Gabs and other side adventures heavily imply that Yuma and the other Master Detectives were in Kanai Ward for a few weeks if not months and thus probably eaten a meat bun or two if only out of curiosity because everyone in town, including their own boss, sings their praises. The player even has the option to have Yuma buy and eat one at certain points in the story. And if Yuma’s reaction was any indication, they probably wont take learning the specific meat that’s used well at all. Not to mention the possibility of some of said human meat containing diseases which might be spread onto the people who eat the buns.
Exactly how did the United Government get some of Number One's DNA? Especially since he didn't know about the experiments at first.
What happened to the bodies of the Master Detectives who died on the Amaterasu Express? Most likely, they were dumped into the restricted area with all the other corpses, and their bodies were stripped down to the bone by the zombified homunculi. The other option is that their bodies were turned into meat buns, since they had human flesh (if a little charred) and were already long dead. Either way, there's very little chance of them being able to get a proper funeral service.
Things become even more dark when one considers they were probably transported as one large group of corpses, which for the Peacekeepers' convenience included the humans and the fake Zilch. Meaning it's highly likely he ate at least some of their remains. Even after death he still continues to torment them.
The end of Chapter 2 has Yomi ordering Martina to be placed in a presser to be crushed into a cube. That's a horrifying fate for a human, but Martina is a homunculus that is supposed to resurrect after a day. What would have happened to her if she were to revive in that state? Would she even revive at all?
The Nail Man killings of Chapter 1 look gruesome, but the crucifixions are all postmortem with the real cause of death being strangulation- except for the fact that they were all in Locked Rooms where the Peacekeepers could not possibly reach the bodies in a timely manner. So, why didn't any of the bodies ressurect into zombies? Answer: They did, but they were all nailed down and simply died again from the crucifixions. This explains why there is an absurd amount of blood for postmortem wounds- it's because they're not 100% postmortem. Indeed, the only victim who WASN'T fully nailed down for the sake of the Locked Room trick bled way too much for the short amount of time it took to set up the thread- implying the victim did likely sit up again on his own at least once before he was discovered. Indeed, Yuma even remarks that the bodies would be pinned down even if they could rise up again, unaware of just how likely that possibility is.
It's not hard to see from the flashbacks that as Number One, Yuma was a lot closer to Makoto in personality, though he was genuinely meant well. We also know that One bluntly states that emotions have no place in detective work, and from Makoto we know he had a savior and loner complex to the point of nearly cracking from the strain of juggling so much in his head and distrust of everyone around him, and amneisa turned him into a sweet natured kid. Just what happened to him?
Many people have pets in Kanai Ward, and given no animals are known to have had homunculi made from them, such pets must be the originals whose owners were killed and now are in the care of their unknowing killers.
There are many elements of existential horror when one considers how the things the homunculi of the city lived for, defined themselves by, and sometimes even died for, were in many cases not "theirs". The Yakou we meet did not have a wife who was killed by an Amatarasu assassin, the Kurumi we meet never had a grandfather; indeed no one native to Kanai Ward even has a history going back more than three years. They simply have the memories of the people who actually lived all those things, people who all died horribly at the hands of the beings who now carry their memories.
Considering all Makoto needed for his plan to replace Number One of the WDO completely was to kill him and usurp his position, and he was already the CEO of Amaterasu Corporation, would he have just let the remaining Nocturnal Detective Agency members die in Kanai Tower too? He would've been above even every Master Detective of the WDO, since he'd serve as the organization's leader... and those that he'd be able to lead would've been the Master Detectives who'd rank lower than him in that situation, that including Halara, Desuhiko, Fubuki, and Vivia. However, the four of them already fulfilled their purpose for him (ousting Yomi) and he'd have no pragmatic reason to release them, unless of course, his affable side happens to be retained, but considering he'd likely be Drunk with Power, that's an unlikely possibility.
Makoto is the one overall responsible for everything that happens in the game, likely including the Peacekeepers' rabid behavior still continuing even after they were replaced with homunculi; but one must remember he's still the CEO of a corporation. And to count up all of his villainous deeds, he's highly manipulative, deceptive, a straight-up liar, a kidnapper, a blackmailer, a cannibal, and a rogue clone of the WDO's hyper-intelligent leader, who is also the only one — the only one — aware that the citizens of Kanai Ward are defective homunculi created thanks to Dr. Huesca and his fatal egotism regarding his scientific achievements, which is something he intentionally keeps a secret from everyone else. That, and considering he introduced Yakou to Fink, he also basically let the only detective chief in Kanai Ward kill his own head researcher under the manipulations of the Peacekeepers' director (all of whom he's their superior to) as part of his own elaborate plan; basically meaning he's completely fine with letting chaos of that level happen between his own subordinates. His level of corruption is immense for just one man leading a corporation considering all of the things that he's responsible for and that he's taking advantage of his identity as Number One's clone.
Why did the fake Zilch not just kill Yuma? Why create an elaborate scheme to fool Yuma into thinking everyone had died and frame him for the crime if the hitman was working with Amaterasu Corporation anyways? It would’ve made no difference if he was killed with the others or framed for the massacre and likely executed by the Peacekeepers regardless. He even drank the laced coffee and was left perfectly vulnerable in the bathroom, so there’s no excuse that he’d be any harder to take out than the other sedated detectives.
Given how Yakou is able to intimidate the Peacekeepers into letting Yuma go with the threat of further WDO involvement, it seems that for all their brazen behavior Amaterasu was worried about going too far and wanted to at least have a small measure of plausible deniability in being involved in the murders. Thus the opportunity to frame someone was something to be taken advantage of. The circumstances of the train being sealed the whole trip also arguably necessitated that there be one person alive to have committed the murders.
Since homunculi are mostly in their more aggressive forms in the presence of sunlight, it is likely most of the casualties from the Blank Week Mystery may have occurred outdoors. The perpetual rain machine would not only remove the sunlight to stabilize the homunculi's conditions, but it can also wash off the human blood splattered around on streets and buildings.
