Case Closed/WMG

Agasa is the Boss of the Black Organisation
This troper is shocked that this wasn't already on here. Think about it. He seems unusally knowledgeable in the first few chapters about what the Black Org will do to Shinichi when they find him, and steers him towards a more harmless avenue than he might have taken on his own - namely, working behind the cover of Mouri as opposed to tracking the BO down outright. Also, he appears to be a kooky inventor. How the heck does he fund all this stuff? Shinichi himself says that half the time his 'inventions' don't work (although that can be taken with a grain of salt, seeing all the spectacular gadgets he's put together for Shinichi, and the time he was comissioned to put together a bomb to blow an abandoned building up for the government).
 * Volume 12: Agasa was able to sell his voice-changer tech to Bandai.
 * Ano Kata's phone number sounds like the song "Seven Children." Agasa's pretty friendly with kids: Conan, Ai, Ayumi, Mitsuhiko, and Genta make five. Then could Shinichi and Ran make seven? In flashbacks Agasa has been seen spending more time with Shinichi and Ran than their own parents do, driving them around on cases and taking them on trips, just as he does for the Detective Boys now.

David Xanatos from Gargoyles is the leader of the Black Organization.
In fact he purposely shrunk Shinichi as phase 12 of his convoluted 47 part plan.

Subaru isn't just Bourbon; he's Ano Kata
During the Pisco sequence, Shinichi correctly realized that the 4869 part of APTX-4869 was a reference to Sherlock Holmes. As Shiho noted, that's pretty odd for a group whose members are typically goons like Vodka and Tequila. Now, let's see...a fan of Sherlock Holmes who sets off Shiho's Black Organization awareness sense...The potential's there. This is also a great mask for him; who'd expect a new hire is actually the boss?
 * I kinda thought Subaru was Akai Shuichi in disguise. Why else would Conan let him into his house so readily? And Conan definitely knew something was up about Shuichi's 'death.' I don't believe he actually died.
 * Subaru being Anokata, at least, has been Jossed--retroactively. In a 2006 interview, Aoyama revealed that Anokata's name had appeared in the manga. Subaru didn't appear until 2008.

Ayumi is Anokata
Anokata is most likely Ayumi Chan, after taking APTX 4869. This theory is the most favored by experts. Some experts however still subscribe to the theory that it is either Yusaku Kudo Kun or Agasa Sensei, but they are in the minority due to recent evidence in Ayumi Sama's favor. This is in contrast to the utterly ridiculous fan theories that Vodka or Gin might be Anokata, or that an as yet unrevealed character might fill that role, ludicrous as that may sound. Popular fringe theories include Jodie Starling, Akai Shuichi, and Haibara Ai; although these theories aren't as outright insane as the theory that Anokata simply hasn't been introduced yet, there simply isn't as much evidence for them as the Ayumi or Agasa theories.
 * Theories that either Kazuha Chan or one of the Detective Boys (other than Ayumi Chan, for which there is of course ample evidence) are also quite popular, but experts hold that they have in fact been disproven. Some disagree and acuse the experts of hiding evidence. These people also tend to fall into the utterly ridiculous camp of people that believe that Kazuha loves Heiji and Ran loves Shinichi, rather than the much more logical and reasonable Kazuha/Ran and Heiji/Shinichi theories.
 * Well, that's the point of WMG. Deny the obvious, uphold the inane, right?

Vermouth is Ano Kata
It's in the name. Vermouth's real name (or so it seems) is Sharon Vineyard. Vineyards are where grapes are grown and grapes are used to make wine, which fits with the naming scheme of the BO. She pretends to just be the Boss's favorite though because she's worried that otherwise one of her underlings would try and assassinate her and take her place. She gave Conan the Boss's phone number on purpose because she's hoping he'll follow through and lead her to everyone all at once, which is also why she doesn't rat him out. She was disguised as that serial killer in New York to feel out how big of a threat the FBI could be, and killed Jodi's father personally because he was just that good. And how she's currently staying young is running out, so she's looking for a new source of immortality, hence the BO's seeming focus on immortality.
 * Of course, there's the problem of the text she receives from the Boss warning her that she's taking her leeway too far. Then again, this could have been part of a masquerade to make Shinichi think she was just an employee if he woke up early. The Vineyard name meaning still works, though, if Vermouth is the Boss's sister, cousin, or wife (i.e. both Vermouth and the Boss carry the Vineyard name).

Black is Ano Kata.
The org's name literally is The Black Organization, named after its leader.
 * But TBO is only the name Conan gave them to call them something, it's not the group's real name.

Gin actually slightly changed the recipe of the drug.
My guess would just be something like sugar, or something else of no consequence. It was put there in case Haibara (A.K.A Sherry) escaped and tried to create an antidote.

APTX-4869 halts aging
The regression effect of the drug not only reverses the aging process but until cured effectively halts it as well. Those who experience effects don't grow at all. Comic Book Time has prevented this from becoming noticeable but eventually there will be a story arc where one or more Detective Boys have growth spurts and leave Conan and Haibara in the dust. This also opens up the possibility that...
 * This is the only theory that makes sense, since otherwise after taking the pill to return to his normal age, Shinichi would not regress to Conan again unless the substance was still present and active in his blood. Thus it would mean that the drug, still active in the body, is effectively halting any aging the two kids may want to do.

Vermouth has taken APTX-4869

 * Because she was much older than Shinichi & Haibara, it didn't de-age her into childhood, merely young-to-mid adulthood (enough she could impersonate her own daughter). Why she did it and why the Black Organization doesn't know about the regression effect are harder to say. It could be that, like Haibara, Vermouth was attempting suicide and lucked out, and either her looks didn't change drastically enough to set off alarm bells, or they all attribute Vermouth's younger appearance to her disguise talents and narcissism. The possibility Vermouth has taken the drug also leads me to think...

There is a specific trigger to APTX-4869's regression effect

 * The two confirmed shrink-ees and one possible all possess one thing in common: They are highly intelligent and near-or-outright masters in their chosen fields. This leads me to believe that the regression effect of APTX-4869 is not a Million-to-One Chance, but has a specific trigger, most likely some genetic trait or something else DNA-based that also creates high level intellect in those who possess it. If someone with this trait takes the drug, they won't die. Of course, this leads to yet another possibility...

APTX-4869, or at least one of its predecessors, was crafted specifically to benefit Vermouth

 * Getting just enough apoptosis out of the body to reverse some aging without getting yourself killed probably depends on the agent being very picky about what genetic material and/or cells it does and does not go after. If the agent was designed to specifically keep Vermouth alive, it's a fair bet that it wouldn't be so pleasant to anyone without some of her own genetic material. Of course, that leads to... Shinichi and Shiho are blood relations of Vermouth's to some degree (see below.)

Vermouth did not de-age with APTX but with Pandora
Alternately, instead of having de-aged with the drug, it could be argued as mentioned above that the BO had once been in possession of the stone Pandora - that cries tears of immortality - and that, and Vermouth was one of the few privilaged who took the serum. Once they lost the stone, scientists like Miyano and his family were brought in to try to recreate the serum. Research included Shiho going to the  to check out all immortality rumours.

This would also tie in to Kid's Organisation being the same as Shinichi's above, and would mean that they could ultimately be forced to join ranks.
 * Which, may I say, would be made of awesome.

APTX-4869 was derived from the same stone that the Arrows from Jo Jos Bizarre Adventure were made from
Great boon if you can handle the effect, near-instant death if not...does this ever sound familiar. Although this troper wouldn't be surprised if the reason Shinichi keeps running into murder and theft cases is because a semi-dormant Stand keeps steering him towards loci of rancor and envy...

Ai has already figured out the antidote to APTX-4869, and is withholding it from Shinichi.
Or she will have in the future, and then keep it from him until the (eventual) end of the series. She could be doing this for two reasons: 1) Because she knows that if Conan finds out that he can be Shinichi again full-time, he would rush to take it and blow their cover, or 2) Because she's in love with Shinichi/Conan and doesn't want him to be with Ran. My guess is that she's telling herself it's the first reason, but there's more of the second reason in there than she'd like to admit.
 * Would also go nicely with the theory that Ai is Ano Kata (see above)...

APTX-4869 is a 'failed' eternal youth serum.
I think it's been confirmed that the Black Org is searching for the recipe for immortality. That's probably what Ai Haibara and any other Black Org scientists were researching. And it seems clear that Vermouth found a de-aging substance somewhere along the lines. So, what if APTX was an attempt at an eternal youth serum, but instead the Black Org realized that it killed people without leaving a trace of how they died? So they started using it as a poison, not realizing that they had come closer to an eternal youth serum than they previously realized: in extremely rare cases (such as with Shinichi and Ai) it actually does de-age the recipient by about 10 years. This would explain both how the Black Org came across such a poison, why the poison did what it did to Shinichi, and why the Black Org believes Shinichi to be dead.

APTX-4869 was specifically aimed at Shinichi
Not exactly much in the way of direct evidence, but there's the possibility that while Shinichi was watching Vodka's deal, Gin (offscreen) was receiving a message from the Boss permitting him to field-test the apoptoxin in case he had to bump someone off. In this case, it would be a direct response of the Boss seeing Shinichi witnessing Vodka's transaction, and intending Shinichi specifically to be Apoptoxin Guinea Pig #1. The problem is that this implies that the Boss has been shadowing Shinichi, and planning to have Gin and Vodka (or anybody else they could entrust with the apoptoxin) administer it when Shinichi inevitably notices some sort of Black Organization wrongdoing (read: pretext for administration). As for why the Boss would think to aim at Shinichi in the first place...Well, I am the one who placed the WMGs about Shinichi and Shiho possibly being related to Vermouth and/or the Boss...

There is no permanent antidote. Instead, Ran will de-age to be with Shinichi.
There is no antidote and there never will be. All growth to one's normal age will only ever be temporary. So eventually, Ran will have to take the APTX to de-age as well, be the same age as Shinichi and they'll grow up and old again. (That's still asuming she'll find out within the next 600 chapters or so...)

The 'Special Gene' required to survive APTX-4869 is an above-average intelligence.
Think about it. 4869 can be read as 'shi', 'ha', 'ro', ku', if you read only the first syllable. Run it together and you get 'Sherlock'. Shinichi and Shiho both have high levels of intelligence, in other words, they are 'Sherlock's.

Conan is followed by a sympathetic Shinigami that provides new cases.
The only murders that are real are ones like the Driven to Suicide ones and the Black Organization Cases. Seeing as how Japan's Real Life murder rate is nearly nil...
 * So it's only a coincidence that everyone they run into has a crappy relationship with their friends or family?
 * Yes, dysfunction is everywhere.
 * Conan manipulated the families into those situations, always picking one person towards whom all the evidence will point, so that Mr. Moore would have a case to "solve". He might have even hypnotized the sucker so that they would believe themselves to be guilty.

Mouri knows where murders are going to take place ahead of time and secretly directs his family to be in the right place and time
Mouri is actually a member of a internet forum or bulletin board network where murderer's announce their intention to commit crimes ahead of time and challenge people to catch them. Clues to this theory are Mouri's admitted use of bulletin boards in his youth, his computer on his desk in the present that he never uses when anyone else is in the room, his wide range of old freinds that he spontaneously decides to visit just before their murdered or murder someone and his love of publicity and media coverage. Inspector Megure is actually far more intelligent than he appears and is secretly investigating Mouri's participation, he will often let slip his suspicion when he first sees Mouri at a crime scene he has no logical reason for being at.

The actual timeline.
While I've only read less than half of the series, a personal theory I've had regarding the progression of time is this: Only about half of the total chapters are true canon. To elaborate, several mysteries are often not referecned again, unless it somehow tied into the main plot or events directly continued from the previous chapter. While I wouldn't know if multiple seasons have passed in main plot related chapters, my guess is that most of the "mysteries" are just filler because the creator probably didn't want to rush to the end or drag out a single mystery too long (the Black Organization/Kudo's return to normal body, notwithstanding). Some mysteries (like the ones relating to Ran/Rachel occasionally getting suspicious of Conan) are meant to happen, as we know that Conan's mission is to get Richard/Kogoro's fame up so he'll attract major cases. It's not a strong theory, but it might help sweep away from confusion.
 * Related theory: The "filler" cases are dreams - Conan/Shinichi is certainly big enough of a mystery geek. Or perhaps they're part of a manga that Dr. Agasa works on in his spare time...?
 * Alternatively, they're part of a novel Shinichi's father works on, inspired by his son's fate.
 * Certainly an interesting theory with the dreams. As I said, I don't know how many "seasons" (and I mean the weather seasons) have "passed" but it would more or less explain how nearly 1000 murders/mysteries have occured and been solved. Only the ones that are extensively mentioned later on/have ties to the Black Organization are actually from the timeline, while everything else is simply filler/dream/what-if scenarios meant to flesh things out (kinda like how you can ignore roughly half or more of Cowboy Bebop).
 * It could be that there are multiple timelines. The continuity-important cases are true across all timelines, while the filler cases happen in one/some but not in others, and are distributed evenly so each timeline is roughly the same length.

== The reason they keep stumbling into mysteries is simple. Conan distracts people with Adorably Precocious Child antics, Ran kills someone with her karate, while Mouri "solves" the case, pinning the blame on some shady person and using his reputation to make it stick == This explains everything.
 * What about the cases with Agasa and the Detective Boys? Who kills the victim? Ayumi?

== Kudo (and maybe Mouri) has something (a curse? Some quirk of genetics?) that causes anyone subconsciously thinking of murdering to act on it. That's why there's always a murder when they go out, even though the crime rate in Japan is supposed to be low == That is all.
 * The only problem is that a lot of these murders require a lot of planning in advance. They can't all be spontaneous.

Alternatively to the above: Conan & Mouri don't attract murders. Murders attract them
They have some sixth sense about when and where murders will take place, and are subconsciously led to where they will occur so they'll be able to solve the crime. On the other hand:
 * Since so many of these murders are acts of revenge for a prior death, the spirits of those original victims reach out to people who can potentially prevent their loved ones from committing murder or, failing that, exposing them and making them try to repent.

Detective Conan chronicles every murder committed in Japan.
Japan really does have a low crime rate; Conan just happens to be involved in solving EVERY murder case in the country.

Giygas is the reason for the ridiculous numbers of murders in the DC universe.
Let's face it, the number of murders in the series is ridiculous. Ignoring the kidnappings and the one instance of suicide, there have been over 600 in roughly the span of a year (since Conan hasn't aged much). And murders aside, the people in the cases aren't the nicest of people. They're usually mean, spiteful, and lashing at people who are supposed friends.

Think about what Buzz Buzz told Ness back in Earthbound. Buzz Buzz said, and I quote, "From now on, you'll be fighting enemies sent by Giygas, as well as humans who have evil thoughts. They'll definitely make trouble during your adventure. Animals are also becoming violent due to Giygas' influence over the evil in their minds! It is the truth, so listen!" To summarize, Giygas' influence takes the evil in the minds of animals and humans and amplifies it.

So what if that influenced human was on the short end of the stick? What if, say, they were cheated on by a lover or were lied to and used by a supposed friend? Suppose they thought briefly of murdering that person in their anger and, after thinking over it a bit, started to embrace the thought and plan it out...

So somehow, Giygas survives the battle with Ness and flees across space and time to the DC universe. Which is good news for Conan/Shinichi, since he wants to be a famous detective.

Ai will not go back to her 18-year old self.

 * Think about it: What's left for her? The Syndicate was her whole life. She has no family to go back to, and she has a pretty good life with Doc Agasa and the detective boys. This is a chance to start over and use her talents for good.
 * Totally agree! I've thought about this too. I think she'd be much happier staying as Ai than going back to being Shiho.
 * Imagine yourself at 18 and turned back into a 6 years old kid. Would you want to go to school all over again? Not to mention that she's a genius, she'd be bored to death. Furthermore, she can't go and show that she's a prodigy, since then the Syndicate will know her identity right away. So, pretty much, she's gonna be pretending to be a normal person for life. Not a good life, I think.
 * She doesn't seem to exhibit anything near the same level of boredom Shinichi has as Conan, though. The social side of things (Friends like Ayumi& the boys) may serve to counteract the boredom from the academic side.

Shinichi actually died from the poison and Conan is just pretending to be a great detective.
Doctor Agasa is insane and his inventions only work in the minds of the detective boys. Mouri Kogouro is actually a great detective and actually solves all his cases. Conan is just a relative of Shinichi's who Kogouro adopted and who likes to pretend he's the one really solving the cases, and Kogouro plays along. Hattori is just plain stupid and actually believes that Conan is Shinichi. Ai is also just playing make believe with Conan. Ran has selective amnesia and doesn't remember that Shinichi died.
 * So how does Conan have all of Shinichi's personal memories and knowledge?

Conan's poison darts change a little each time.

 * There is no way that watch has so many, so he has to get refills from Dr. Agasa. Because he is worried about the effects of it in the long-term, like whether it might kill someone or stop being effective, he changes the sleeping recipe slightly each time Shinichi shows up for a refill.

Haibara is lying about the terror thing.
Haibara has said to Conan that, if he should tell Ran exactly what the hell is going on, then she'll be terrified. Now, this contradicts what she says about the strength of someone's feelings for a person affecting how they act with that knowledge. Look at Yukiko, Yuusaku, and Agasa's reactions. They don't believe him, but they help him hide. Ran would probably beat the crap out of him and then calm down and help him through the series later on.
 * Haibara said that before she knew anything about Ran. She's since re-evaluated her opinion. Now her objection will most likely be, "She'd want to get involved, and that would get her killed faster than you can say 'Ano Kata'."

Shinichi and Heiji are not Meitantei
Or, at the very least, aren't as good as they'd like to say.

This is a simple idea. The only person who had heard of Shinichi from the Kansai area is Heiji, and Shinichi had never heard of Heiji before he showed up. If Shinichi (who is considered the better of the two) is the savior of the Japanese police force and known to be such, then why aren't other areas and countries attempting to get him to solve their cases? Thus, they are just two high school students who solved some cases and got inflated egos.

This also can relate to what Kazuha is thinking when she first sees Shinichi. She thinks, So this guy really exists? Please note that she is best friends with a detective who has knowledge of Kudo, and has mentioned him repeatedly. But since she never heard of him, besides (assuming) after Volume 13 of the manga, Shinichi has an inflated ego.
 * Shinichi does have an inflated ego but he does show the ability of a good meitantei. Shinichi has been called to other areas in the past too - movie 1, that manga case with the village that hates him - it's their lack of concern towards that pesky thing called school that is a concern. (Though Shinichi at least has an excuse during the main time period.)
 * This may have been discounted in a recent chapter where the culprit or an attempted murder held a grudge against Shinichi, and subsequently had collected an impressive number of newspaper articles with said detective's solved cases enough to cover an entire wall.
 * Well, do you know any real life detective? Even if there is actually a genius detective like Shinichi in real life, no one would have a clue about him. This career doesn't have a large popularity, so it's understandable that only people in legal and crime force will know about Shinichi and Hattori.

Shinichi has a drinking/drug problem
Deconstructing on the above, Shinichi tried to be a great detective and failed, this depression led him to drinking/drug usage.


 * He drank so much it resulted in brain damage changing him into "a childlike state"


 * When things get really bad (getting a cold) Drinking/Drugs is his only way of feeling better (being Jimmy) He longs for it to work when he is not this way too and has attempted bt nothing can bring him out of his depression.

The Black Organization are Freemasons, the Illuminati, Skull and Bones Society, the Knight Templar, and/or Lizard People.
Why do you think they can achieve such secrecy? They have control over the banks, the politicians, and the media without no one knowing it. For all we know, Obama, Bush, Gates, Rockefeller, and Jay Z are all part of the Black Organization. Only Conan can stop the New World Order.
 * The Black Organization are actually Patrio. . . La-li-lu-le-lo.
 * The Black Organization is a faction of the Soldats, Ran Mouri is a potential Noir.
 * The Black Organization is backed by Seele, everything in Detective Conan is moving toward the Second Impact.
 * The mysterious Boss of the Black Organization is Seele 05

Teru Mikami is an alternate universe version of Eri Kisaki.
Besides the whole gender thing, they're very similar. They both wear glasses, are extremely successful lawyers, the main protagonist knows not to mess with them, they both have long hair, ect. But Teru is insane, while Eri is not.

One of the kami is answering a prayer Conan made when he was very young.
He wanted to become the world's greatest detective. This kami therefore steers Conan in the direction of imminent murders (because practice makes perfect), and intervened to let Conan and also Ai defy the odds and survive the rejuvenation process.

Not only is the Black Organization (or at least Gin) fully aware that Shinichi is still alive, but they probably never actually wanted to kill him.
Think about it. We know Gin is a professional killer. We know he usually doesn't make mistakes when he is killing people. But when, in the first episode, he gives Shinichi the poison that turns him back into a child, Gin is acting completely amateurish. Instead of making sure that Shinichi really is dead, Gin and Vodka just poison him with a previously untested drug and run away. That is just too unprofessional for them - except if Gin never actually wanted to kill Shinichi.
 * This is handwaved as Gin and Vodka having just cleared themselves of being murder suspects earlier, and they were in a hurry to leave. Plus the drug does have a ridiculously high fatality rate. They didn't count on Shinichi having Plot Armor.
 * Wait... Why does Gin tip his hat in deference when he doesn't do the same for Pisco?
 * I don't really understand your question.
 * While I like this theory, Gin and Vodka aren't aware of any million to one chances, as far as I can tell Haibara is the only one aware of the secondary effect, everyone else just thinks its a poison. Gin might know better though, since he is high up in the organization (at least it appears that way) and obviously the drug was developed for other purposes than just poison. It's also possible that Agasa, the true head of the Black Organization (see below) told him about it.
 * It seemed to me that the Black Org never actually wanted Shinichi dead; he just stumbled on a case and they gave him a poison which had a 1 in a million chance of de-aging someone instead of killing them. So Gin actually does believe Shinichi to be dead.

Haibara is either a deliberate Captain Ersatz of Dana Scully or is an Alternate Universe version.
Think. They both have similar appearances (short, auburn hair; Scully is much older, while Haibara has been de-aged, though), they are both scientists, they both use sarcasm to deflate a co-worker's insane ideas, Haibara was affected by APTX, whereas Scully was, their co-worker is obsessed with something that ends up being involved with their work, then there's the Shipping... There are so many similarities, I'm waiting for the Black Oil virus to show up in Detective Conan and there being an alien invasion.
 * Haibara isn't an Alternate Universe Dana Scully, Haibara is the Dana Scully.

Conan & the Kaito Kid are related.
This is a fairly old one, to judge by the amount of fanfics based on it. Even laying aside the art style, Shinichi Kudo & Kuroba Kaito (and their respective parents, who are basically them with moustaches) are basically identical - even to the point of Shinichi's not-girlfriend Ran mistaking Kaito for Shinichi in the street. In addition, whenever the two butt heads with one another, much is made about how closely matched they are. The theory normally runs along the lines of the magician Toichi Kuroba (secretly the first Kaito Kid) introducing Yukiko Kudo (as she is known by the time of the series) to his brother (and occasional sparring partner) Yuusaku Kuroba, who legally takes up his pen-name of 'Kudo' after his brother's hounding (and eventual death) at the hands of a mysterious mafia-like organisation.

The Black Organization and the mysterious group chasing Kaito Kid are the same people.
Considering that Pandora's Jewel (from "Magic Kaito") sheds 'tears' every time a certain comet passes the Earth that grant the drinker immortality, and the fact that, I think it's fairly likely that if the Black Organization is the same as the group from Magic Kaito, the reason they need money and a large syndicate is to steal as many gems as they can to find the true Pandora's Jewel. Also, it may be possible that either a) the BO's leader is already immortal, and that's why his phone number is a child's song and is finding the Jewel for a lover, sickly child, trusted right-hand man, etc., b) is using Vermouth's knowledge of the gem to help track it down for him/herself, or c) Pandora's Jewel has another secret power we don't know about.
 * It seems clear that both groups are after immortality in some form.

Shin'ichi is really dead and Conan is his replacement.
Conan's a copy of his six-year-old self sent into the future to fill in Shin'ichi's spot in the universe when he died unexpectedly. Similar circumstances exist for Haibara.
 * So why does Conan have all memories of Shinichi, as if they were his own?
 * Memory implant. He's supposed to be a full, if short, replacement, after all.

Shinichi is actually making the antidotes last longer than they should.
All of the antidotes were only supposed to last a short time, but because of Ran he tells his body to make them continue. It's kind of like a placebo effect.

Kogoro is a millionaire.
In an early episode there is mention of a fee of 500,000 yen for Kogoro's detective service. There have been over 500 episodes. Assuming he gets paid his fee at lest 250 times throughout the series (many of the episodes are in two parts or don't involve Kogoro, so 250 is a conservative estimate) he should have made 250 x 500,000 Yen = 125,000,000 Yen. According to Google that equals 1.38875 million U.S. dollars. Now, since as far as I can tell (I haven't seen any recent episodes yet) he hasn't moved out of his apartment and spends all his money on beer, he can't possibly be lower than 1.3 million dollars at this point. This is exasperated by the fact that time doesn't seem to pass in Detective Conan.
 * That doesn't seem to be a set fee, though--Kogoro is seen to receive a piggy bank full of money in return for helping a child star), and Kogoro is seen to be VERY irresponsible with his money, blowing through a good chunk of a similarly sized fee in one of stories. Additionally, we don't know if Ran is attending a public or private school (private seems much more likely, given that her classmate Sonoko is from a wealthy family, and Shinichi also lives in a Big Fancy House) and we also are unaware of the circumstances of Kogoro's separation from his wife. She's probably not asking him for alimony, but one never knows.
 * Given the dynamics among the Mouris, chances are Eri gave money for "Ran's living," which of course include her tuition at Teitan.

Vermouth was in New York City in 1930 at the induction of Firo into the Martillo Family
...and she drank the booze that Isaac and Miria provided.

Kogoro KNOWS Conan is Shinichi
It's been established that for all his bumbling, Kogoro can be a very good detective under the right circumstances. In fact, it's been stated that he could even be as good as Conan when motivated properly. He's had who knows how long to notice all the clues to Conan's real identity, clues his daughter has also noticed at times. His motivation would be seeing how worried Ran is over Shinichi. In fact it's likely he noticed said clues even earlier than she did, but ignored them due to his characteristic laziness. But once they started piling up enough, he finally caught on. So why has he been so quiet about it? It's possible that he somehow caught on to the fact that Shinichi is hiding his true identity for a reason]] (again, he is much sharper than he often seems) and has just opted to keep mum about the situation. His hitting Conan on the head all the time for involving himself in the investigation is a form of revenge for all the times he's been put to sleep by the kid.
 * Perhaps he hits Conan on the head because no matter what, his pride cannot take that a little kid, whoever he really is, is stealing his shine.

When Ran confront Conan about his identity again, he will tell her that Shinichi is his older brother
Think about it. Both are detectives, both tend to stick their noses in other peoples deaths. And both have tendency to end up solving murders and all. They both smart, and know things that their not supposed to. So telling Ran that Conan and Shinichi are related is way easy to believe, than that Shinichi is drugged and de-aged.

Ran knew all along that Conan is Shinichi.
Well, Conan is just like Shinichi, and because of that, Ran has easily figured that out from the beginning. However, when she heard him saying that she's gonna be killed by the Black Organization if she found out, Ran has decided to follow this and pretends not to know that Conan is Shinichi until he gets a chance to tell her about it.

By the way, the occasions of Ran making Conan confess his secret and the latter tries to get the former to ignore the idea are just only a ruse for Conan not to know that Ran knew his secret all along.

Heiji is only pretending to be clueless about his feelings for Kazuha.
At first he was only pretending in order to annoy her and because he was embarrassed, but after he met Conan (especially the Desperate Revival and the arc where he and Kazuha were kidnapped) and seeing Conan's struggles, he started to truly realize how dangerous it was for a detective to be romantically involved and keeps up the act partly to keep Kazuha from getting even more involved with him and partly out of respect for Conan who can't be with Ran.

Shiho is either the daughter or niece of Vermouth.
This is in allusion to my earlier point about Shiho (and Conan) being blood relations of Vermouth's to some measure. Also, consider that although we haven't yet heard their finish, the last we hear of the cassettes left to Shiho by her parents sounds like the stock build-up to a revelation that she's actually adopted. Adding in the possibility that a genetic trigger is necessary to keep you from being killed by APTX-4869, it becomes very likely that Shiho was "rescued" from her actual parents by the adoptive ones; she may well have been at risk of being treated like a guinea pig or something, to see how much genetic drift can remain before APTX-4869 winds up killing you. Vermouth is an obvious candidate for this mother. However, if Subaru really is the head of the Black Organization, the possibility emerges that he's Vermouth's brother, and also that Shiho might instead be his biological daughter.

There will be 108 volumes of the manga.

 * Prepare for waiting for a long time.

Subaru is MI 6
Gosho Aoyama already did the whole, "They're an Organization member! NO THEY'RE NOT!!!" thing with Jodi, so it almost seems obvious that he's not a member either. But he's probably not FBI or CIA because we've already had characters from there introduced, and we already know that they're involved. Possibly he IS still Bourbon, but he's a double agent like Kir. And it was a little random that the Mouris would be invited to London by a random rich and well connected lady who lost her cat. Maybe it was on purpose so that agents could observe Conan a little less obviously (stranger in a familiar place versus stranger in a strange place). Maybe the woman is simply an employee of the British Government.

Subaru is actually...
A member of the KGB, but is not Bourbon. Bourbon is actually Akai, who's been convinced somehow to become Bourbon by the Black Org. Or, Subaru is both KGB/the modern Russian spy unit, and is Bourbon, but the reason why he hates Akai is that Akai was approached many years ago to be a Russian spy within the FBI and the Black Org, but he refused and killed the agent that approached him, who was a friend or blood relation of Subaru. Hence why he, as Bourbon, hates Akai more than even Gin.

The reason no one's aged in however-many episodes/chapters...
... is because a Time Lord did it. A Time Lord could have been just plain bored and decided to see what the long-term effects of a time-perception field could be. Thus we have six hundred-plus episodes really taking place over at least a decade. However, the Time Lord's time-perception field has its targets (in this case, Conan's town, country, or even the whole world!) not noticing that time is passing, while at the same time preventing their bodies from aging. Nevertheless, technology marches on - we get cell phones, etc. The time-perception field is just preventing people from noticing that something's afoot.
 * Alternately, it doesn't have to be a Time Lord. Any creature with command of space-time could be behind it.

Shinichi will have a Heroic BSOD momment when he comes across something that he can't explain...
Such as meeting Akako from Magic Kaito and discovering that her magic is real, or coming across an actual ghost.
 * Then he'll know how Battler feels.

The real identity of the detective girl Sera is...

 * A relative of Shuichi Akai. With the way Aoyama Gosho's art style looks there happens to be a lot of similar looking characters, but from a certain point of view, Sera's facial structure is similar to Shuichi's.
 * Really Shuichi Akai is Sera. After being "killed" by Rena his only option to hide from the Black Organization was to change his identity and get a sex change. That's the reason Sera is so flat chested, it is because she's used to be a man. It becomes clear why "Sera" deleted the video that caught a glimpse of Haibara off the internet; it was naturally to protect the little sister of his dead lover. And why the other three FBI find "Sera" to look slightly familiar is because his real identity is Shuuichi.
 * Apparently Jossed as of issue 801.  The previous theory is looking better, though...
 * A girl Shinichi met while he was in America. She stated outright that's where she is from her first introduction. Naturally she being a fellow mystery lover, she fell in love with Shinichi, but only now decides to go find him in Tokyo. She might be bi-sexual, and wouldn't mind a OT 3 with Ran, Shinichi, and herself.

Okiya Subaru is Akai Shuuichi.

 * Mentioned above somewhere, but needs it's own entry.
 * Both Okiya and Akai give Haibara the chills she gets from members of the Organization.
 * Despite that, Conan trusts Okiya enough to let him stay at the Kudo house. "No fan of Sherlock Holmes could be bad" is really not a good explanation, and if it's "friends close, enemies closer", he could have said so. Furthermore, Conan goes beyond letting Subaru stay at his house; he lends him the keys, asks Okiya to pick him and the kids (including Haibara) up, help out with cases a couple times, and more.
 * They also just plain look similar, so that all Akai would need are glasses and a wig, or he could dye and straighten his hair. They wear similar styles of clothes, too.
 * Ran seemed to think Okiya was familiar the first time she met him, having previously encountered Akai three times.
 * The names in Detective Conan almost always mean something. Akai means "red", and in the "Red, White and Yellow" case, Okiya Subaru was the "red guy".
 * In issue #800, Okiya says "Don't make that kind of face" to Haibara. In issue #802, she remembers Akai using the same phrase while undercover as Moroboshi Dai.
 * In issue #810, Okiya says he can't force Haibara to come with him, "because of [a] promise he made her..." If he is Akai, then he could be talking about Akemi Miyano.
 * Which then implies he knows who Haibara is.
 * The Detective Conan Wiki has expanded this theory.
 * New theory: Okiya Subaru is Akai AND Bourbon. Akai went and reinfiltrated the B.O. under a different identity.
 * Jossed as of chapter 821;