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A collection of fan speculation sourced from tropers and reader comments. Beware unmarked spoilers.

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    Pandora 
Shinichi is the source of the Pandora Effect
Hakuba and Yuusaku act as if they are afraid of Shinichi's powers and Hakuba seems alarmed by the idea of Shinichi learning anything about the "disaster" they're "keeping a lid on," and especially by the fact that Shinichi has heard the term "Pandora Effect" before. Hakuba's dialogue also implies a connection between Shinichi's presence and people around him losing control of their emotions and becoming lethally violent, which lines up with what we hear of the Pandora Effect. Yuusaku and Hakuba know this and are trying to protect Shinichi from the Awful Truth.The second interlude confirms that this is what Hakuba believes and what Yuusaku has told him, at least. Time will tell if it is true.

The Pandora Effect is the result of Shinichi's abuse
Shinchi implies his powers are effected by his emotional state. It's possible the Pandora Effect has been getting worse over the years both because his powers are getting stronger as he gets older and because the abuse has gotten worse, making him more emotionally unhealthy.
  • If it's connected to Shinichi's emotions, why did riots only break out in chapter 12? Why not in chapter 9, during Shinichi's confrontation with Yuusaku, the only scene during which Shinichi becomes antagonistically angry and confrontational (as opposed to his quiet, restrained, resentful anger seen in other chapters)?
    • Maybe it was due to the pain of whatever turned him into Conan in this universe?

Yuusaku caused Shinichi to cause the Pandora Effect
Yuusaku is repeatedly erasing memories of Shinichi's more potent powers from Shinichi's own mind, decimating Shinichi's chances of learning to control them and causing them to go out of control when he's emotional without him even realizing they exist. The psychometry and empathy parts of Shinichi's abilities were just too obvious and ever-present in Shinichi's perceptions to erase, because he'd notice they exist again almost immediately. Similar to above, the other forms of child abuse Yuusaku enacts onto Shinichi means Shinichi's increasingly in emotional turmoil as he's gotten older, leading to the Pandora Effect as an everyday background influence getting steadily worse.
  • Further, we know three relevant things about how Shinichi's mental state relates to his powers: 1). Shinichi's emotions effect his powers' strength and manageability 2). Shinichi's powers are a major source of emotional and psychological stress at the best of times, and 3). Yuusaku has attacked his son for years in a manner that could only have made his emotional and psychological state worse. QED: Regardless of whether Shinichi's powers are as destructive as feared, the only logical conclusion is that Yuusaku's choices have been a net negative on Shinichi's ability to control them.

Yuukiko and Shinichi are the source of the Pandora Effect
Yuukiko was heading home just as things went crazy at the end of Part 1. Yuusaku informs Hakuba in Hakuba's flashback that Yuukiko and Shinichi together is correlated with severe emotional fluctuations in those nearby. It's possible she was nearby for the KID vs. Baron incident eight years ago. The combination of the two emotion-affecting powers controlled by two contrasting wills exuding two different effects probably causes the mental and emotional instability reported.

Yuusaku and Yuukiko are the source of the Pandora Effect
And not in a "technically true because they had Shinichi" kind of way. Shinichi being the source of the Pandora Effect kind of works timing wise, but his powers as so far demonstrated are the opposite of the Pandora Effect: he absorbs others' thoughts and emotions. And while there have been instances in which Hakuba and Yuusaku attribute correlation as cause, Shinichi has yet to concretely demonstrate the actual necessary ability to alter someone else's emotions or thoughts, even when he wants to; his parents are the ones who do that. And given the illusion and secrecy they enforced, to the point of deliberately not helping Shinichi with his powers and pretending he didn't have any... did anyone actually check to see whether Shinichi was even capable of causing thabe Pandora Effect, before jumping to the implied assumption that he is? If anyone in the Kudo family is the source of the effect, it seems more likely to be the parents.

The Kudo family is toxic and create the Pandora Effect when all their powers combine
Insert Tuol's Captain Planet joke here.

Pandora as it is currently understood in the story isn't actually real
Its effect actually is the result of complex socio-economic circumstances. Or, if metagenetics are involved at all, the circumstances are far more complicated and interwoven than something as simple as a single cause. Hakuba's thoughts about Shinichi's powers are a Red Herring.

Pandora is a Meta-Organism, but not a human one
Shinichi's brief flashback of the night Toichi dies mentions a red gem, just like Pandora is in canon. It's possible Pandora is actually some kind of gem-like organism, or even just another kind of organism, rather than a human being. It's mentioned that metagenetics occur in animals and plants as well, after all, and that the occurrence of meta-abilities has increased greatly just in the last few decades, which could point to the influence of something else at play.

Pandora is a kind of parasite
It was the red gem, but the expression of its abilities gets absorbed into other organisms. It was first absorbed into Toichi, so Yuusaku killed him, but then it was absorbed into Shinichi, proving that killing its host doesn't work. Yuusaku has since been seeking a way to nullify the expression of Pandora's abilities instead.

Yuusaku and Hakuba think Shinichi is the cause of the Pandora Effect, but are mistaken
There's no evidence so far to support Shinichi being connected to the Pandora Effect aside from a few coincidences of timing during events implied to be associated with Pandora. Yuusaku himself admits that even the assumption that Yuukiko and Shinichi together are causing mental health strains on those nearby is mere correlation... right before suggesting he doesn't think it is, with no evidence for the audience.

Yuusaku wants Hakuba to think Shinichi is the cause of the Pandora Effect, but is deceiving him
Word of God has implied that Yuusaku was putting on an act in front of Hakuba to convince Hakuba he actually cared about keeping their secret identities secret from Shinichi. In actuality, Word of God has brought the truth regarding Hakuba's assumptions about Yuusaku heavily into question. It's clear the thing most keeping Hakuba in line with how Yuusaku treats Shinichi is the painful secret Hakuba thinks he knows about Shinichi, heavily implied to be the belief that Shinichi's presence makes people violent. Yuusaku is a Consummate Liar and Unreliable Expositor obviously trying to control people; it's possible this suspicion was introduced to Hakuba to limit and control Hakuba's behavior and interactions with Shinichi. Notably, Hakuba's implied belief that Shinichi unintentionally manipulates emotions has caused Hakuba to withdraw from Shinichi and become exceedingly cold and emotionally unavailable to him. Hakuba openly admits during Yuusaku's conversation with Officer Date that, were it not for Yuusaku telling Hakuba earlier that the truth was different, Hakuba would be unable to tell that Yuusaku was lying to Date, because Yuusaku has no tells that Hakuba can perceive. Hakuba boasts about how he is one of the special few so trusted by Yuusaku and how Yuusaku lies to everyone else but him... but if Yuusaku lied to him, how would Hakuba ever know?
  • Circumstancially supported by Hakuba's portion of the second Interlude. The Pandora Effect completely stopped after the fifteen minutes of riots and hasn't been felt or perceived since, which appears to have (from Hakuba's perspective) convinced Yuusaku that Shinichi died. However, we know Shinichi isn't dead. This leaves two possibilities: that whatever turned him into Conan disabled Shinichi's metagenetic phenotype, or that Shinichi himself wasn't the direct cause of the Pandora Effect.

Yuusaku does believe Shinichi is the cause of the Pandora Effect, and has set Shinichi up to self-destruct
Instead of giving Shinichi a non-dangerous outlet for his desire to investigate and help people, Yuusaku blocked safer outlets and denied Shinichi training for self-defense skills or with his powers, and further, has actively eroded Shinichi's ability to seek help from other people. He's gotten everyone from the police to his closest loved ones to act as if they are dismissing what Shinichi says, decimating Shinichi's trust in the authorities that he should have been able to trust to help him. We know for a fact that Shinichi has no back-up and, when he feels he's doing something life-threatening, only leaves a vague note on his blog about where he's going so interested parties can go looking for him if he disappears. Yuusaku has done this because he's accepted, on some level, that Shinichi is on a collision course with disaster regardless and can't be saved. He's given up, retreated from being emotionally attached to Shinichi, and subconsciously wants Shinichi to get himself killed so Yuusaku can tell himself he didn't have a direct role in his son's downfall. His abusive tendencies are also an expression of him subconsciously wanting to punish Shinichi for the position his existence has put Yuusaku in.
  • Addendum: This is because Yuusaku sees himself as victimized by his son's existence and has made the tragedy of the situation mostly about himself. This is a possible interpretation of Word of God comparing Yuusaku to the poor beleaguered men in Hesiod's version of the Pandora myth who have to suffer through coexisting with women, who are a plague and a curse upon them.
  • The end of Part 1 is the plan Gone Horribly Right. Just at the moment Pandora could credibly be ended without killing Shinichi, the wheels Yuusaku set in motion—his untrustworthy behavior, constant roadblocks, depriving Shinichi of key information—mean that he doesn't learn about this solution until it's too late, and things are already at a crisis point. To Yuusaku, Shinichi (presumably) dies just like Yuusaku planned... right when Shinichi's and hundreds of other deaths could have been avoided had Yuusaku not kept Shinichi ignorant and continuously roadblocked.

Alternatively, Yuusaku is trying to prime Shinichi to accept blame for the Pandora Effect
Regardless of whether some part of Yuusaku genuinely thinks Shinichi is the cause or not, some part of Yuusaku still feels guilty about Toichi's death, so he's trying to prime Shinichi to accept that Toichi's death is Shinichi's own fault and accept the blame from Yuusaku should Shinichi ever find out that Yuusaku and Hakuba think he, Shinichi, is Pandora. Yuusaku doesn't actually know for sure, but being able to blame Shinichi helped Yuusaku cope, and eventually developed into a self-affirming frame of mind.
  • Alternatively, Yuusaku is trying to prime Shinichi to accept blame so that Shinichi blames himself for the abuse, rather than holding Yuusaku accountable for his terrible actions. Originally Yuusaku hid his suspicions about Pandora thinking it would spare Shinichi, but eventually he was forced to face the reality that the effect of the secret on Shinichi's life was possibly just as if not more painful and destructive in the long run than just telling him years ago and supporting him through processing that. Yuusaku has coped by avoiding Shinichi and telling himself that it's For the Greater Good and that Shinichi and others would understand if only those poor ignorant people knew the truth, but Yuusaku must heroically bear the consequences of their ignorance for their own good. Yuusaku's now staunchly against telling Shinichi about Pandora because he's afraid of Shinichi finding out and refuting his Freudian Excuse, tearing down his protective delusion of righteousness and leaving no refuge left for Yuusaku to morally justify his terrible actions.

Hakuba wanted the Meta-Nullifier for use on Shinichi
Hakuba says Yuusaku trained him to solve the problems Yuusaku can't. Hakuba probably thinks this problem is that Shinichi is Pandora, and to blame for what happened during the KID vs. Baron fight eight years ago. Hakuba thinks that if ISHA discovers that Shinichi is Pandora, they'll kill him to protect others just like they did Santa. Ultimately, Hakuba thinks the purpose of all of their lies and controlling policies is to protect Shinichi above all else, and so believes the ultimate goal of them attaining the Meta-Nullifier would be to use it on Shinichi.
  • Basically confirmed in the second interlude.

Pandora isn't something that causes violence, it causes Power Incontinence
In canon, Pandora is said to instill immortality, and the goal of APTX 4869, the drug Miyano Shiho creates, has been figuratively associated with immortality (well, with "raising the dead against the stream of time"). Perhaps, if the drug that causes Power Incontinence in the kidnapped children is Miyano Shiho's Crows-funded project in this world, then Pandora also follows suit and causes something similar. In which case, the "Pandora Effect" is not innately mass chaos, and the fact that it results as such is simply a coincidence. The Pandora Effect is just unknown person(s)' abilities being altered and/or going out of control for brief spans of time, and those person(s) affected by "Pandora's" direct amplifying effect happen to possess, somewhere along the line, the ability to alter others' states of mind, which is what actually causes the mental and emotional effects on nearby populations.

Shinichi's other power isn't mental manipulation, it's Super-Empowering
Similar to above. If Shinichi is the cause of the Pandora Effect, it's obvious he has to have some power we don't know about yet to mentally and emotionally drive people all over the city to commit irrational and dangerous behavior. But if Shinichi can alter people's minds like this, as far as we know, we haven't seen it. There have been plenty of instances where, even unknowingly, you'd expect Shinichi to unconsciously use this power to get his way, and thus for people to cooperate with him more, but nothing is further from the truth. And if Shinichi is the source of the Pandora Effect but doesn't have the powers that seem necessary to cause it, how is it happening? By boosting those around him. Kudo Yuusaku, famously on the scene for the Baron vs. KID disaster, does possess mind manipulating abilities. Kudo Yuukiko possesses emotion manipulating abilities, and wouldn't you know, people's emotional states go out of whack when she's near her son. Hattori's emotional response when Tequila hurts Shinichi and Hattori punches Tequila in the face in return isn't out of character for Hattori—he's hotblooded, overprotective of his friends, and seemingly obsessed with becoming Shinichi's BFF—but what is considered strange is the power he puts behind the hit. Hakuba seems to assume Hattori's emotional state was abnormal in that moment, but it could literally be that there was just more power behind the punch. It's possible that in these instances, Shinichi is boosting the powers of those around him without realizing it, and those individuals happen to have powers that affect others in the manner associated with the Pandora Effect.
  • This would explain why the Crows want Pandora. If Pandora is chaos, then it might be a means to an end, but Chaos is rarely an end goal (unless it's the end goal of a madman) because there's not much benefit in being in a perpetual state of chaos. Chaos is good for knocking things down, but you need relative stability and order to shape the aftermath how you wish. If the Crows want to cause chaos for the sake of disrupting and destabilizing current power structures, they would need to know how Pandora works in order to predict it and deal with its aftermath to bring order to their own end of things, because chaos is only good for an evil plan when it's someone else in chaos, not you. And if Pandora is Shinichi, it seems like it'd be hard for them to know that much about how the Pandora Effect functionally works, considering Hakuba and Yuusaku are so secretive. But if they somehow figured out that the nature of Pandora is actually Super-Empowering and the chaos is merely a secondary effect, then they can predict how it will work depending on what it empowers.
  • It would also, thematically speaking, explain why Shinichi is treated more like an object to protect than a person. He'd be a Living MacGuffin.

Shinichi's other power is passive influence
It helps him get people to cooperate with his aims. This is why Yuusaku does his best to set up competing loyalties to disrupt Shinichi's passive influence over others. And this ability might be interfered with somehow in a way that creates the Pandora Effect.
  • Circumstancially unlikely. We see Shinichi try to influence people while interviewing them in his reporter role; it probably would have been easier to get what he wanted if he had some innate superpower for it.

Pandora's "curse" is retribution for, or a consequence of, an "unfair" advantage gained by humanity
In the legend, Pandora's existence was created as the wages of humanity deceitfully gaining from the gods without due payment. Word of God even refers to Pandora and the curse interchangeably on their blog as "the price for fire," and notes that the narrative deliberately parallels the myth in specific ways. It's possible that, like the myth, this world's "Pandora" was the figurative or literal consequence of someone overstepping their boundaries for humanity's perceived gain. Perhaps "Pandora" is the payment for whatever has caused the huge upswing in the occurance of metagenetic organisms, or perhaps, if Shinichi really is Pandora, it's a consequence of one of Yuusaku's "brilliant" attempts at heroism in his youth, paralleling him with Prometheus.

    ISHA 
Someone high up in ISHA is an agent of the Crows
And the Crows were the ones who ordered to missile strike on Santa and Shinichi. The fact is, the higher ups of ISHA had little to no information exchange with Shinichi's group and had previously shown no actions demonstrating an awareness that the "disasters" were caused by the missing children or where these children were, yet ISHA knew exactly where Santa was to send the missile.

ISHA is actually being puppeteered by the Crows
Forget one higher up ordering the strike—it's Evil Running Good. What with grooming of child soldiers and air striking victims, does it sound like ISHA actually cares about anything more than keeping the populace docile and stable for the sake of keeping things under their control? If this is true, Santa and Shinichi would have been targeted by ISHA even if Santa's powers had been nullified, because Santa, Shinichi, and Hirota were the only witnesses to the Crows introduced at that time who weren't under ISHA's control.

ISHA is not being puppeteered by the Crows, but is still bad
ISHA as a whole being secretly genuinely malevolent would be too simple for this story; if they're anything like their trainees or the real-world police and military then they probably have a mole or two, but it's more likely they overall have well-intentioned leadership that wields a lot of power and so is capable in a crisis but simply sucks at actually being ethical about it. Given how 'little regard the ISHA-associated members of the cast show for actual human rights violations, ISHA's real evil is probably more banal, like not recognizing labor laws, child protections, universal human rights, or the concept that war crimes are something they shouldn't commit (not gonna forget that Hakuba was younger than eight, ISHA!). The fact that their only oversight appears to be self-regulating and internal also doesn't instill confidence in their morality, given how well self-regulating internal oversight has gone for maintaining the ethics of law enforcement, governments, and big corporations the world over. Any allegedly benevolent world power that thought calling themselves the Overseers was a good idea clearly has an F in good, no involvement by murderous crime syndicates necessary.
  • It turns out anti-meta activist Karasuma Renya was the one who coined the term "Overseer"; however, the public didn't fully get the negative coding of the word and both they and the operatives accept and use it thenselves.

Sato is the new ISHA operative they're sending to work with the TMPD
The new operative is Jinpei [Matsuda]'s partner. She hasn't appeared yet because she was "neck-deep in Korean terrorist cell during Part 1 and was sent ahead to Tokyo after the Black Hole Crisis, missing the ISHA meeting that features her partner Jinpei in the Interlude.

The Undertakers will be investigating Yuusaku and the Irregulars
Given the unclear nature of Shinichi's involvement with this disaster and the fact that he exposed ISHA's shady side to the entire world, undoubtedly creating a PR fiasco to go with their internal affairs mess during a time already implied to be very tense when it comes to the subject of ISHA and its power, the Undertakers will want to start their investigation with Shinichi's friends and family, which are, of course, all ISHA associates. This will start off a kind of cold war between groups, in which the Undertaker operatives want information that Yuusaku is trying to obfuscate, because the truth of Shinichi's involvement in the False Kidnapping Incident is messy and a problem but it would also undoubtedly reveal an even bigger mess of Yuusaku and Hakuba's not-so-professional behavior and the fact that they and the ISHA mole at the police station turned away Shinichi's intel on the very situation that developed into the Black Hole Crisis and, through their refusal to validate his information, put him in a position in which he felt morally forced to act on his own, a position Hakuba and Yuusaku put him in all for seemingly no reason. Ignoring intel is the kind of thing people in law enforcement get canned over, especially when that negligence results in a diminished capacity for law enforcement to do its job or in casualties, and this resulted in hundreds and was capped off with the very public disappearance of the whistle-blower himself. It may even be through interviews with the Undertakers that we the readers find out what story Yuusaku and the Irregulars are going to be telling and how they feel about everything that's happened in hindsight.

The Undertakers will be tasked with executing the remaining experimented children
Jinpei does describe them as the "leash and shotgun" that removes any of ISHA's messes from the public eye.

Rebound is Makoto Kyogoku
He's 18, quiet, formal, polite, intelligent, very brawny, and a bit naive—fits the characterization of Rebound perfectly.

Override is Matsuda Jinpei
Counterterrorism, suppresses bombs.

Eradite is Akai Shuichi

Shriek is Mizunashi Rena
  • Jossed. Turns out Shriek is Sato Miwako.

Minerva is Kisaki Eri
Minerva is the Roman god of wisdom, defensive combat, and war tactics. Through her Greek predecessor, Athena, she was also associated with maternal guardianship and the court room, as she had the deciding vote on the Athenian jury and famously oversaw the court trial of Orestes. As long as they're referring to a superhero alias and not the actual Minerva Glass, the Superhero Minerva is likely smart and tough, and we know she's the equivalent of Yuusaku's rank. Of the adult female characters around Yuusaku's age, there's only a handful that would befit the intelligent, dignified, yet intimidating alias Minerva. Plus, Shinichi mentions that both of Ran's parents were Meta-humans, and given how Shinichi says metahuman registry usually just functions as a program to usher kids into ISHA, it's very likely Ran's parents have some connection with ISHA.
  • Ran mentions in chapter 12 that her mother works in ISHA's legal department and has level two authorization; this is presented as much lower than the Night Baron's, which would contradict the idea that Minerva is Eri, considering Minerva is treated in-context as something akin to the Baron's equal in rank. Of course, Ran could also be uninformed about her mother's full job.
  • Likely Jossed. An ambassador comments on how Minerva is the national hero of England. This would point to Minerva Glass, except it's strange that she would use her real first name.

    Miscellaneous 

Hakuba is actually the one Yuusaku wants to control
Consider: Yuusaku is seemingly doing everything he can to antagonize Shinichi into hating him. Same with Kaito. Only an idiot wouldn't expect them to respond negatively to being antagonized so thoroughly. Who's the one character Yuusaku goes out of his way to continuously manipulate into staying on his side, despite everything? Hakuba. Who's the character Yuusaku apparently championed from childhood despite his comparatively less useful powers? Hakuba. Who's the one he taught to suppress emotions and blindly trust in Yuusaku's authority? Hakuba. And yeah, Yuusaku says he wants to control Shinichi. And yeah, Yuusaku is plenty abusive to Shinichi. But he hasn't gone about controlling him in a smart way, if controlling Shinichi is his goal. Shinichi's too smart and too stubborn to control through force. Yuusaku and the Irregulars have functionally made themselves his antagonists trying to forcibly subdue his will. His mind may be vulnerable to the damage of an obvious attack, but it will not surrender to one. But people are open with trusted allies infinitely more than enemies, a fact Yuusaku is perfectly aware of, given the situation with Aoko and Kaito. And yet Yuusaku has only ever acted as Shinichi's enemy to Shinichi's face. Yuusaku has incentivized Shinichi more and more to close up to those around him, to resist the impulse to reach out and open up and trust others. It's Hakuba to whom Yuusaku behaves as a trusted ally and with whom he actually tries persuasion and reason since childhood rather than straight authoritarianism, even while manipulating and hurting Hakuba just as much as Shinichi or Kaito—and so it's Hakuba who actually trusts Yuusaku and does his bidding. Yuusaku's not dumb enough to believe coercion would work on Shinichi and he hasn't tried another method, so it's clearly Hakuba that Yuusaku's actually trying to control.
  • Possibly supported by the fact that we see him do this with the Irregulars when their team's status quo is threatened by internal conflict over Yuusaku's behavior. Yuusaku doesn't try to provide an explanation for his actions to Shinichi and does his best to instill the clear message that Shinichi is beneath being explained to. It's unclear if Yuusaku genuinely believes this, but in contrast, he does actually go out of his way to attempt to explain to the Irregulars a more humanizing reason for his antagonistic behavior towards the son of his victim—proving he knows how to deescalate an argument and just chose to escalate it with his son anyways, implying he's encouraging Shinichi to be antagonistic with him but still wants the Irregulars to accept Yuusaku's behavior enough to maintain the functionality of his relationship with them as their superior—and, tacitly, their allegiance (as opposed to siding with Shinichi and ignoring Yuusaku's orders, which many of them were very close to doing before Yuusaku interrupted).

Yuusaku intends for his son to hate him
Just following through with the above logic. We see him "rationalize" similar behavior with Kaito, although it's unclear how true those rationalizations are, but the effect of antagonizing Shinichi into hating him is pretty obvious.

Kuroba Toichi invited Shinichi to his last heist to kill him
Regardless of whether Shinichi is Pandora, since KID's canon goal in the manga is to destroy Pandora, Toichi, under the impression (as so many of the cast appear to be) that Shinichi is Pandora, invited Shinichi to his last heist to kill him. Yuusaku killed Toichi in a struggle to protect his son, and really has been trying to help Kaito in his own warped way by letting Kaito hate him rather than letting Kaito know that his father really did intend to commit murder. The trauma of the circumstances has led to Yuusaku taking things out on Shinichi, as Yuusaku wants someone else to blame for the situation and Shinichi makes a perfectly convenient scapegoat.
  • This has some entirely circumstantial support in the implication that some event we haven't heard of yet had to have initially upset Shinichi the night Toichi died. If we accept that an aspect of Shinichi's powers is causing the Pandora Effect, and operate on the supposition that Shinichi's emotional state causes him to lose control of his powers (as he heavily implies when he compares how his powers to Santa's), the Pandora Effect that night was likely kicked off by something upsetting Shinichi to the extent that he lost control of his abilities. The question is, what initially upset Shinichi that night, and upset him to the extent that this night was different from any other instance of upset prior? Further, why did the Pandora Effect impact Toichi in particular, when he's the one character on the scene that we know is allegedly resistant to the influence of psychic powers? While any number of possibilities could explain the seperate odd implications that Shinichi became upset in a way different than any upset prior and that Toichi got the full brunt of the Pandora Effect, if Toichi did something upsetting to Shinichi and got hit with the full force of Shinichi's power in response, that would explain both unusual occurances.

Yuusaku lied to Hakuba about Shinichi's powers
Whatever powers Hakuba thinks Shinichi has, it's clear he thinks they have to do with affecting others when they're upset and that he thinks they are dangerous. However, Hakuba notably doesn't seem to understand how Shinichi obtains certain information, an answer for which would obvious if Hakuba actually knew Shinichi's powers. It seems obvious that Hakuba isn't as aware of the "truth" as he internally proclaims.

Conan will become a respected investigator
This story works on inverting a lot of the premise in canon. Since we know Conan's going to show up in Part 2, that Ran and everyone treat Shinichi in Dominoes like they do Conan in canon, and that grade school Child Soldiers are apparently an accepted thing in this world, it's possible there will actually be less stopping Conan from attaining respect and success as an investigator than there currently is for Shinichi. Bonus points if Conan encounters Ran and Ran complies with Conan's investigations instead of scolding him.

Conan will go live with Kaito
Since he can't stay with Ran this time.

Conan will end up living with a minor character from the series
He can't really go live with any of the main cast without them knowing and trying to control him again. He'll probably end up getting taken in by someone "new."

Yuusaku discourages Shinichi because Shinichi is actually more powerful than him.
I can't see Yuusaku being the kind of guy who takes kindly to people more powerful than him.
  • Shinichi's abilities are classified as 'S' rank (the highest), but Yuusaku's rank is redacted.
  • Circumstancially supported by the fact that, in spite of Yuusaku's disparaging comments about Shinichi, Hakuba (Yuusaku's chosen Number Two, the person Yuusaku passed Shinichi over for) is actually the member of the cast most like Shinichi... except for one major difference: Hakuba's meta-abilities appear to be the weakest and most superfluous of the current cast, a far cry from Shinichi's intimidating "S" rank.
Alternatively...

Yuusaku discourages Shinichi because he thinks ISHA could use Shinichi against him
If we discard the possibility that Shinichi is Pandora, we're left with the fact that Yuusaku has gone out of his way to prevent others from knowing about Shinichi's powers and prevent Shinichi from learning how to control them. Despite being an ISHA operative, he never bothered to register his son's powers in their database (which, despite Shinichi speaking as if this was his own choice, would be Yuusaku's and Yuukiko's responsibility as the parents of the minor in question), thus depriving Shinichi of the training that registration would have provided. Yuusaku also gave his son no support and, it seems, had everyone hide the fact that they too had powers from Shinichi, making Shinichi feel as if he had to go it alone when it came to managing his powers because it wasn't worth registering with ISHA. If Shinichi isn't Pandora, the only explanation is that Shinichi's powers, should he learn to actually control them and should ISHA learn of them, would actually single him out for something. This troper believes that, disregarding the possibility of Pandora, that something is intelligence assets. Shinichi's abilities are basically the superpowered form of the Sherlock Scan with even more information tossed in. He can leaf through someone's life story from a handshake, feel the history of an object's use by the brush of a fingertip, see the long-over events that occurred in a room by touching a wall. As far as we can confirm right now, his powers seem literally perfect for investigation. And Yuusaku has done his best to quash the effectiveness of those abilities. Should ISHA learn of Shinichi's powers, Shinichi could be a security breach in Yuusaku's life, a way for ISHA and others with whom Shinichi chooses to work to learn things about Yuusaku that he does not want others to know.
  • Possibly, ISHA could try to induct Shinichi into the Undertakers, a job Shinichi, objectively, is terrifyingly well-suited for, given his abilities would enable him to know very quickly the who, what, where, when, and why of any screw up. If Shinichi isn't Pandora and Yuusaku has indeed covered something up without telling ISHA the full story, Shinichi is a potential major threat on Yuusaku's control of things in the future because he could very well become the perfect "leash" for Yuusaku if given the proper training and chance.
  • This would also make sense with the author hints that Yuusaku doesn't actually care if Shinichi finds out their secret identities. It wasn't about depriving Shinichi of information, it was about depriving Shinichi of support. That's why Yuusaku makes his speech afterwards as brutal as possible and immediately after plays to gain the Irregulars' sympathy and thus their support, which would have the functional consequence of depriving that same support from Shinichi. Notably, he doesn't care to make the same kind of efforts to make peace with his son. If this is true, alienating Shinichi wasn't a side-effect of trying to "protect" him, it was the goal, and "protecting" him just provided an excuse to cut him off from further contact with any group of metahumans that could supply alternative support.

The story takes place in 2021
Because April 2021 lines up perfectly with the weekdays and corresponding dates described in the story. It could also be 2010, but everyday technology seems closer to 2021. (Not that that means much, considering they have hoverbikes).

Yuusaku actually can erase Shinichi's second-hand memories.
Despite Shinichi concluding Yuusaku can't completely erase memories Shinichi absorbs from others, this doesn't fully add up. We know Yuusaku can't use his powers on KID's mind and never could. Both of the memories Shinichi believes Yuusaku cannot fully erase actually come from KID. If Yuusaku could not erase any second-hand memories Shinichi absorbs, then how could Yuusaku possibly have kept Shinichi as ignorant as he was for so long? Even accidentally, Shinichi should've come in contact with a second-hand memory that blew one of the many secrets around him; the Irregulars have been frequently in and out of his home since the group formed specifically for the purposes of ISHA activities, and Hakuba's been Shinichi's surrogate brother for almost a decade. It's possible the only memories Yuusaku can't erase are only immune to erasure because of Kaito's Ripple-Proof Memory, not because of any feature of Shinichi's powers.
  • Alternatively, during the False Kidnapping Incident, Yuusaku comments that he can't feel Shinichi's mind and that KID could've found some way to extend his mental protection to Shinichi. It's possible this protection is still in effect even afterwards. After all, how else could KID be sure that Shinichi wouldn't be a security link for KID's secrets? We know Shinichi has come to know a lot Yuusaku doesn't since the night Shinichi made his temporary alliance with KID, and since then, not only has Shinichi managed to maintain his knowledge of those and the Irregulars' secrets, but Yuusaku has failed to take secrets from Shinichi's mind, such as knowledge of KID's spider robot that Shinichi dropped in Yuusaku's office. Shinichi assumes that this is because Yuusaku was only taking surface level thoughts, but this isn't true; in fact, it's heavily implied Yuusaku used his powers to force Shinichi to hand over his evidence without Shinichi even being conscious of this until afterwards. In short, how much power Yuusaku has over Shinichi mentally appears to be inconsistent throughout Part 1.

The Irregulars and their Mentor mirror the Seven Deadly Sins
While the set isn't complete, as no one yet fits Gluttony or Lust, the remaining Irregulars and their mentor each represent one of the classical flaws.
  • Aoko is Wrath—she seeks to make another suffer for personal reasons and lets her spite towards them control her and cloud her judgement. This pushes her into Black-and-White Insanity to the point where she eventually refuses to acknowledge help from or good qualities in anything or anyone associated with the subject of her fury, to her own detriment.
  • Ran is Greed—a non-monetary example. She wants the career and she wants the boyfriend and she's somehow missed the fact that they're incompatable because she wants both. She also covets her boyfriend like an object, and only prioritizes herself, her desires, her needs, her terms, and her feelings in their relationship, giving him little to nothing in return.
  • Kazuha is Envy—she's deeply jealous of Shinichi because Hattori admires him so much, and this skews her ability to feel empathy and her relationships with those who care for Shinichi.
  • Hakuba is Sloth—he alternates between being genuinely unable to recognize when he needs to take action and being Willfully Blind and practiced in feigning apathy towards suffering when he actually recognizes he's complicit. He's learned to ignore the feeling that he's not doing what's right... to terrible results.
  • Yuusaku is Pride—or at least, this is what he ''projects.'' He insists he's superior, that only his methods and practices are right, he derides contradicting opinions and mocks the idea of his son ever being able to hold a candle to his own capabilities. Pride goeth before the fall, whether projected or not, as choosing not to hear out anything Shinichi could've told him turns out to be a horribly lethal mistake. Of course, depending on what's actually going on with him beneath his facade, it's possible he's actually the Orthodox Church's Eighth Sin, Despair.
    • Mirroring how he eventually quits the team, Hattori proves himself the odd man out. While flawed, he's not particularly controlled by the Classical flaws and instead demonstrates the Virtues corresponding directly with the Classical Sins of his Character Foils. He shows Charity in contrast with Ran's Greed, as Hattori sees Shinichi's need and personally sacrifices to support him, and Diligence in contrast with Hakuba's Sloth, as he refuses to remain an Accomplice by Inaction.
    • Similarly, Shinichi, as Yuusaku's and Hakuba's character foil, also represents the Virtues to Hakuba's and Yuusaku's Sins. In this case, Diligence and Humility. The point is made, repeatedly, that no one and nothing can stop him from doing what he wants—especially not from doing what he thinks is right. And unlike Yuusaku, whose boasted achievements are narratively still an Informed Attribute and whom continues to insist on his superior intellect, Shinichi has not only fully demonstrated his capabilities under pressure in the story, but learned from the pitfalls of pride years ago, considering his mistake with the homeless children to be his deepest shame. And, too perfect to be a coincidence, if Yuusaku is Despair, then Shinichi aligns with the virtue of Hope, the famous last gift at the bottom of Pandora's Box.

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