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Forgive me if anyone has ever talked about this but from my searches I have never seen anyone that has from this angle.
I was thinking the other day about every episode I have ever watched and every manga I have ever read and I started to develop or see a connection in my head that made sense. I cannot name the exact episodes or manga chapters these happened in but here goes: (All episodes mentioned are manga based)
The Black organization's goal is to prevent death.
Besides the obvious statement by Vermouth: "We can be both of God, and the Devil,Since we're trying to raise the dead against the stream of time" But I was never able to place what the Black Organization was stealing with any resemblance of order until I thought about actually preventing death and here is why:
1. to prevent anything you need to know the five W's (e.g. What, When...)  of some data and have a computer program that catalogs the data and statistically arranges them. The Black Organization has on at least 2 instances: Episode 54, Game Company Murder Case where Tequila was killed and Episodes 307-311 where the guy was killed but was also trying to design software, used programmers to design software programs that have a specific use.
2. Once a data processing system is in place a model would be generated and certain people would have to be killed in order to manipulate the model to a specific end. (Episode 425)
3. Besides continuing the series, Conan is involved with too many murder cases that conveniently happen around him. One way to rationalize this in the end to viewers would be (and based off what Haibara said one time, "Kudo-kun? You would probably never even dream that you are already part of a project the Black Organization has been working on already for half a century.") that in order to stop people dying would be to have certain people that unfortunate circumstances happen around and then replace them with people that could prevent those things from happening instead. This would explain why things would continue to happen around him and in more frequency. Because the model is converging deaths on key people.
4. No matter how good your model is things will happen and that is why you have your R&D section develope a way to fix those statistical variances that slip through. In this situation it would be a drug that revives the dead.
5. The organization still needs money so swindling and killing by your controlled group (Gin, Vodka...) is ok because it is a means to an end and justified because of the end goal.
Defenses of this theory:
1. To my knowledge nothing conflicts with it.
2. The goal of the organization needs to be pretty big by 650+ episodes and 800+ Manga.
3. This can be done silently and revealed at the end
4. It is on such a massive scale that it would take a long time to implement (like 50+ years  ;)) and could happen without suspicion as the whole picture is hard to see
5.Its the ultimate curve ball. When Kudo finally understands the end goal and then has a moral debate about how to proceed because the boss might actually have a noble goal.
6. The organization still stands to gain by leveraging governments/companies/organizations that they could drop their protection if they don't give them money. So it isn't completely goodwill. It is just a good goal on the macro-view of it.
7. Only the boss could know the true goal and everyone beneath them could be doing several large tasks that make up a whole while never seeing the end picture (This could still make the current enforcers, gin, vodka..., replaceable.
Please give me your criticism. I cannot read Japanese so I could have missed something completely. And all rebuttals and agreements are welcome.  

This might be a the ends justify the means but if they are trying to prevent death, why use death to cover up their activities? It is a physiologic argument that those who are opposed to killing are unlikely to kill to reach that goal. You are in a way suggesting that the BO is opposed to killing because if they are trying to prevent death, using death to prevent it, is not a good way to do it. What is clear is that indeed the BO does not mind killing and therefore death. So you need to explain more. Are they trying to prevent all death? Are they only trying to prevent certain kinds or types of death? If so, then why just those ones? Are they are okay with bringing the dead, or those who had experienced death, back to life. Does that include those they have killed?

Having the above and seeing your #5 above, you still got a problem. Put it this way: Would the Boss kill the entire world to prevent the death of only one person? If not where is the line drawn? You introduce a slipper slope by using the End... Means Argument. As the Bo boss is very clever, I can not see them going that way, as they should be far seeing and thus see where they are trying to get to and the ends to get there. Also if they will be bring the dead back, will the dead be glad to be back or will they wish they were still dead? Those like that might not be able to redie and thus be angry and slowly go mad. Again, the Boss should be able to answer these question, and again I believe that if the cost is too high, then that route will not be taken. I do not think the BO Boss is a mad man, but instead is maybe too clever for their own good.

It will be interesting to see how this comment is fit into your theory.

There is one thing...I'm pretty sure the manga is huge because it's populaity, not because of the plot, including all the killing that ahppens around Conan.

The most obvious theory is that they are trying to achieve immortality, but anyone can conveniently come up with something else, since there aren't many facts revealed about the organization so far.

sstimson wrote: This might be a the ends justify the means but if they are trying to prevent death, why use death to cover up their activities? It is a physiologic argument that those who are opposed to killing are unlikely to kill to reach that goal. You are in a way suggesting that the BO is opposed to killing because if they are trying to prevent death, using death to prevent it, is not a good way to do it. What is clear is that indeed the BO does not mind killing and therefore death. So you need to explain more. Are they trying to prevent all death? Are they only trying to prevent certain kinds or types of death? If so, then why just those ones? Are they are okay with bringing the dead, or those who had experienced death, back to life. Does that include those they have killed?

Having the above and seeing your #5 above, you still got a problem. Put it this way: Would the Boss kill the entire world to prevent the death of only one person? If not where is the line drawn? You introduce a slipper slope by using the End... Means Argument. As the Bo boss is very clever, I can not see them going that way, as they should be far seeing and thus see where they are trying to get to and the ends to get there. Also if they will be bring the dead back, will the dead be glad to be back or will they wish they were still dead? Those like that might not be able to redie and thus be angry and slowly go mad. Again, the Boss should be able to answer these question, and again I believe that if the cost is too high, then that route will not be taken. I do not think the BO Boss is a mad man, but instead is maybe too clever for their own good.

It will be interesting to see how this comment is fit into your theory.

Let me start off by saying I don't actually believe in this theory. I simply found a couple pieces from different puzzles and I saw my own puzzle and I cannot get it out of my head and I want someone to prove to me I am wrong so I can move on or I will just start compounding the puzzle and making it more layered.
That said I believe everyone can agree that given the length of time in this story that Gosho has put into  Detective Conan and the hype he has tried to generate around this, that the eventual outcome must equal the expectations he has instilled in the readers. Any moderate or childish outcome will completely ruin our invested time and create a lot of angry fans. So the organization's goal must be epic! They can't try and take over a company, they must try and take over a country.
Now addressing your query: (thank you for posting by the way),
I believe the boss in this theory to be like most business leaders, designers, or engineers. And to use the example of building a dam as a comparison. In this theory, I believe the boss has an initial starting point or threshold, kind of the line in the sand , that when all the things are in place they will start acting upon their concerns. When you build a dam you divert the water sometimes and you lose that amount of water that you could have temporarily dammed or stored, but sometimes it is just the way things work/cost of business to accomplish the end goal of a water reservoir or a means of power generation. I don't believe the boss likes death as an end result but is willing to use it to accomplish the end result which according to this theory is an Eden like environment.
Every tyrant in history wants their own 'Eden' and they use whatever means possible to get there because 'the whole is greater than the sum of it's parts' in their own minds.
In this theory, their goal would be to eliminate all death. It is presumed that the Miyano's were working on some mad scientist design to bring the dead back to life. At least that is what I have come to understand from what has been shown so far. That or deriving a compound from Vermouth, presuming she truly doesn't age. Or maybe both bringing the dead back to life and preventing aging.
Do they want to bring back all the ones they have killed?
I would say it depends on the Boss. Earlier when I said it was a line in the sand. Maybe the boss only cares once the entire thing is setup. Does he want to revive all the dead from the beginning of time? We have to look at reality and decomposition rates. Really only if someone is kept preserved can they be brought back to life...that or if they died in the last 72 hours...max, can they be even thought about being brought back to life...and they would be brain dead unless their brain got oxygen that entire time. I believe the boss may initiate a plan once everything is setup to prevent any further death. Bringing anyone not preserved back to life from the past otherwise is simply medically impossible...even in stories.
Would the boss kill the world to save one life?
I don't know if I understand what you are asking here or if I have even answered your true questions up til now or if I have been answering my perceptions of the way I view your questions, but I go back to the line in the sand, the tyrant mentality, and means to an end. You have to crack some eggs to make an omelet. You cannot accomplish the end goal of eliminating death and making a new order without modifying the old order. Revolutions uproot governments by mass or small casualty losses. But there has never been a bloodless revolution. I see your question as limit question. My answer is based on a sum of reasonable returns because the boss has their goal and has predicted the costs to get there and is comfortable with them.
Will the dead like being brought back to life? Problems?
I believed this to be the just of the slew of questions you asked. I honestly didn't even think about this aspect. According to the theory, the organization would offer their services to governments whose job is to protect the people. In light of revolution is the reason why government's would want this service to make sure the citizens didn't revolt from envy of another country who citizens couldn't die. There will always be someone who just doesn't want to fit and desires a way out. I would think life as a gift that most people would want to cling onto. The organization's goal would not be to force no death, just provide a realistic option to prevent it.
My final statement that I believe is the root of all my argument is: I believe some people would do anything for a chance at life. And the organization is looking to capitalize on that and serve the Boss's end true goal and eliminate death because he is driven to his goal with tunnel vision.

BO's aim is immortality for the Boss/Anokata, whether anyone else in the world dies or not they could care less.
APTX reserach is one end, the other is probably connect human mind into a computer AI therefore making his brain immortal and that explains their investment into computer programing.

My reaction when reading the first paragraph on the first post =>

But then I read all the post and the reply 

And my reaction after reading this whole thread =>

wolfman wrote: Defenses of this theory:
...
2. The goal of the organization needs to be pretty big by 650+ episodes and 800+ Manga.
...

for your info... gosho never expect that this manga (DC series) would end up as a BIG HIT! even the anime staff think this will end in 10 or 20 volumes only.

and like all shounen manga that have 2 side opposing each others, the BO is playing the "Devil / Bad guy" role... while Conan playing the "Angel / Good guy" role. simply as that!.

the BO will never aim to bring good to human kind while Conan will try to keep the world at peace.

Please Read this post if you read the first post.
Like I said before I don't believe this theory is true, I just can't find anything wrong with it and that can be explained by leokiko's comment that we don't really know enough about the organization to really say anything for certain.
Oh and I feel like I should clear up the title real quick . I only added the (serious) part because this wasn't a joke. I probably should have said (a serious one) instead.
To respond to ShinRan4ver, I believe the pursuit of a immortality drug would rend the need for a digital replication of the brain to be obsolete. 
I would agree with most claims about the boss if they were not pursuing software or programmers to design code. That throws a wrench in everyone's theory I have read so far because everyone usually overlooks it but there is a greater connection to software code and programming than any other type of interest in the Black Organization's dealings that we have seen so far. (Of course that could be because we only see that aspect because that is the only side that Conan stumbles upon)
To respond to xpon, I chose this angle because of the shock factor that Kudo would have to face at the end. This could also be tailored right into a theory that the organization is tracking everyone's movements to annihilate the human race. The FBI on foreign soil is so completely off that it would have to be a direct threat to United States government. The CIA is believable...the FBI though is historically only a US thing, They usually don't invest their manpower oversees. But more directly to your query about Gosho having an original idea and the fans have caused it to become a big deal, but the original design is still there:
From a story line perspective, I believe Gosho had an original plan. I do believe it changed when he started compounding the story. When he added more characters and plot devices he had to alter the ending to match the new content. The only way he would not have to do this is if the original ending was already on such a massive scale that the influx of characters would better suit it. Right now we have way too many characters to not be a massive scale ending. The only way not to be would be transport the main character away from the primary scene and have very little supporting characters that tag along for the finale. Every author has their own coup de gras or shock moment that is meant to throw everyone off. Gosho could simply have this be the identity of the Boss. That person would have to be insanely well connected to the plot and already visible to create that much of shock value. More likely the boss is perceived to be someone they are not and the plan is on such a massive scale to produce such minute changes over time that it would seem like normal happen stance by the characters (and therefore the readers) until it was revealed to be something much larger and on a massive scale that no one could perceive from looking at one angle. The ideal angle is to have that and then have the Boss have a good intention to throw off the morality factor of the main character to leave questions and engage higher brain function after the series is ended which causes repeat sales as people try and see little nuances that they missed the first time once they see the grand picture.
My theory is one that has been used in MANY plots. You may shun the idea because you cannot imagine Gosho taking this route, but with a day's planning I could name off so many stories that each one of you has read, watched in a movie, or heard about that the list would probably be size of this post. So the theory is not asinine. It just has a shock value that would anger/suprise/reward the fans because Kudo would meet a force that matches his own and aligns somewhat with their own goals but took nefarious methods to reach it. Another avenue of my theory is that the organization wants to kill everyone to make an 'Eden' with the ones they choose to remain. That works in my theory also, it just doesn't have the full shock value that the theory I stated does.
Tell me what you think. I am not saying it's the truth, its just an idea that literary people have used for centuries and they are usually the stories that are remembered.

Red messaged

You wanted a critique, so....

The evidence you offered in support of the theory was not convincing. If I were to summarize, there is nothing in this theory that makes it more likely than any other random theories. To explain what I mean, take the immortality/antiaging theory: that has supporting evidence in the form of Vermouth not aging, the rare side-effect of APTX, Haibara's description of the ingredients and working of APTX, Pisco's confirmation about Ai shrinking being what her parents were shooting for, etc...

1. To my knowledge nothing conflicts with it. - While better than theories with contradictions, this isn't a decent standard to hold a theory to. Shinichi could have been in a coma dreaming of all of DC. Agasa could be the boss. Ayumi could really be a boy.
2. The goal of the organization needs to be pretty big by 650+ episodes and 800+ Manga. Gosho thought the manga would only last a few months.
3. This can be done silently and revealed at the end - How does this support your theory? This doesn't seem to be relevant to me.
4. It is on such a massive scale that it would take a long time to implement (like 50+ years  Wink) and could happen without suspicion as the whole picture is hard to see. - Lots of other potential projects might take this long as well. Why does this theory explain it better?
5. Its the ultimate curve ball. When Kudo finally understands the end goal and then has a moral debate about how to proceed because the boss might actually have a noble goal. - Why is this twist ending more likely than a "normal" ending or another twist ending?
6. The organization still stands to gain by leveraging governments/companies/organizations that they could drop their protection if they don't give them money. So it isn't completely goodwill. It is just a good goal on the macro-view of it. - How does this support your theory? There are lots of reasons why a mafia-like organization may wish to muck around with politics, corporations, etc. Why does this theory explain it better?
7. Only the boss could know the true goal and everyone beneath them could be doing several large tasks that make up a whole while never seeing the end picture (This could still make the current enforcers, gin, vodka..., replaceable. - How does this support your theory? There are plenty of reasons for the boss to be secretive and not share the goal of the Org with most of the rest of it. Why does this theory explain it better?

It seems you are basing a lot of your support on what you perceive to be a good idea for an ending that would shock the fans and turn the entire manga on its head. While you think this type of ending would be the appropriate dramatic finale, Gosho typically does not write this way. He is very predictable and deliberate, aiming for surprising endings, but always laying lots of supporting clues so that people can correctly deduce the ending ahead of time. The idea is that if you are good enough at solving mysteries, you won't be surprised at all. This is typically how single cases and major Black Org arcs go, so I don't see Gosho changing his successful formula for the bigger issues.

First, I want to say thanks for all the thought provoking and well mannered responses. This is my first time ever posting in the forums and based off the topic I kind of expected a backlash if there was any response at all.
Chekov: short response: I agree.
Long response:
"It seems you are basing a lot of your support on what you perceive to be a good idea for an ending that would shock the fans and turn the entire manga on its head." I agree, but I haven't been able to think of a better way to end it that wouldn't disrupt everything (Luckily, I am one person and can be wrong.) And you are correct, (which I did state in my last response) that these reasons/ supporting facts do fit a number of possible outcomes. I am just choosing the one that is the most plausible in most other stories (I'm sure that most people don't agree with that statement but there it is.)

I have thought that this ending is against Gosho's style and to be honest I simply believe that something like this is still possible because authors usually search for these resolutions and place leads that lead up to moments like this in series finales. Like you said Gosho drops hints and he is currently dropping hints slowly that aim to the indentity of the boss and the goals of the organization. I did follow that trail of breadcrumbs and it led me to this conclusion...which like I said is not based off facts and simply put, follows the trend most authors seem to go with by turning the very goal of the protagonist into the eventual goal of the antagonist. In the end, will Gosho fall into the same rut that most authors do? I would like to say: No. At the same time what is there to prevent him? We are all very impressed by his work, otherwise we wouldn't be here. At the same time is there by chance some human factor that we are overlooking that could cause this series to end in a manner we don't like at all?
I do appreciate your invested time to respond. And a critique is always welcome with me. I guess you wouldn't call this a theory, since like you said there aren't facts just postulations, but more of a gentlemen's musings based off the ongoing trend of the outcomes of similar antagonists. At the same time though since the reasons for supporting it also support a wide range of possible actual theories that have more concrete evidence. "While better than theories with contradictions" ...thanks for the compliment. And I have read your accumulated post of all the theories that are supplemented with facts and I must say it is very impressive!

Looks like Chekhov beat me here, but he (she?) pretty much hit it on the head. Your theory is interesting, but your entire defense is the fact that there is no evidence against your claim. Anybody could make claims based on the sole defense that there is no way to disprove what they're saying. I could come up with dozens of theories of my own, but without proof to back them up it would just be random guesswork. That's why I've refrained from posting any theories of my own, and will continue to do so unless I find something tangible to back them up.

Your theory, while interesting, doesn't feel to me like it matches the style Gosho has created. This is a series that, despite some fantastic elements like the APTX 4869, has kept itself fairly grounded and realistic. Whatever the BO is actually trying to do, I doubt they're literaly trying to raise the dead. What Haibara said about "raising the dead against the flow of time" sounds like a classic Gosho smokescreen to me. I'm sure the truth is imbedded deep somewhere in that statement, but we're still missing the pieces to decypher it.

The BO is one of the most difficult facets of Detective Conan to theorize about simply because we know so little about them. Gosho has been careful to give us only the most mimimal amount of information he can get away with about them, which makes it nearly impossible to form any conclusive theories about them. My advice to you, if you really believe in your theory, is to keep working on it. Gather information, revise, rethink, and then get back to us. Once you have some facts to back up your theory we'll be better able to debate with you. As it stands, there isn't much we can say about it. It's basically just guessing, and that's something Mouri Kogoro would do. You don't want to be a Mouri Kogoro do you?

Interesting theory, but as others have said, it's highly unlikely at best. It's hard to theorize on the BO in general much less their underlying motives/end game - especially to such a specific extent. I personally doubt that their end game will have any sense of altruism when all is revealed, but even that's something that can't be stated for certain.

By the way, apt signature is apt.