Case 1: The Pokémon War

The Myth: Well, you're strolling along Kanto, and you suddenly realize something: there are the boys, the girls, the elderly, the woman... But where are the men? Yes, there are some men, but they're generally unhealthy (a.k.a. unfit tonight in a war). Then Lt. Surge comes around saying that his Pokémon saved him during a war! This also means that it happened recently, because he can't be over thirty years old, right? Now, you may be asking, what about all the men gym leaders? Well, they were probably gym leaders before the war, to, right? Meaning they would have stayed there so people could still challenhim the gyms. I mean, in crisis, the best thing a nation can do is try to keep its citizens calm, right?

I also found an interesting theory on /threads/58477-Pokemon-Conspiracy-Theories, and the author was Stryker X7:

"There's a theory floating around the interwebs that paints a dark, horrific history of the Pokémon world, or at least Red/Blue's Kanto region. Many players have noted that in Pokémon Red/Blue, there is a large absence of middle aged men in the game world. Think about the last time you played Pokémon. An abnormally large amount of Pokémon trainers chillin' in the wild were little kids. Think about it. Why were there so many damn toddlers roaming the wilds unattended? There were plenty of elderly men and women in the world (Professor Oak), and many middle aged women (the player's mom, the nurses), but a lack of middle aged men. What about the player's father, or your rival's father? While most people wouldn't worry about the absence of middle aged dudes, some Pokémon fans have rationalized this through the creation of yet another insane theory.

The electric-type gym leader, Lt. Surge mentions being a survivor of some sort of brutal war that almost took his life (he claims that his Pokémon saved his life). Other trainers in the gym were once soldiers in some sort of army, which presumably fought in a war. A war where Pokémon were used as weapons. Let that sink in for a moment, as you try to imagine the horror of hundreds of terrified soldiers storming beaches being held by goddamn Charizards. Some fans believe this war was the cause of the lack of adult men, claiming that all of them had been killed in the war. Essentially, some people are speculating that this war caused a 'generation kill', and that the young children of the Kanto region are the first generation to find peace. This also explains why the player's father is absent (hint, he died), and why the rival character has no parents (hint, they died). While a lot of this theory involves speculation and imagination, the horrifying idea of a human-Pokémon war that wiped out an entire generation is pretty damn sweet."

There was also something interesting on the same board, website, and author:

"You can call this a prequel to Pokemon Conspiracy #11.

January 22, 2027: Dr. Hagiru Sato and his team of scientists from Japan, America, Canada, and Britain begin work on a matter-energy transference machine.

February 11, 2030: First machine is tested successfully after over a hundred failed tests. Controversy over the destructive nature of the technology ignites.

December 21, 2032: A catastrophic incident with an energy-matter machine destroys the city of Hiroshima, in devastation not seen since the atomic bombs were dropped nearly 90 years prior. Japanese government officials move to ban work on the technology, though Western powers urge them to allow it, despite the mishap.

April 22, 2035: First sighting of infected individuals. Most are animals; some humans are also shown to be susceptible to infection. Most seen around the ruins of Hiroshima, which had not been rebuilt.

May 13, 2035: Northern Japan is split off from its Southern half, as a nation-wide quarantine is enacted. Anarchy soon spreads through the infection regions. 15% of humans exposed to the disease are immune, no side effect. 84.9% are affected fatally by the disease, which causes cancerous-growths. .1% of those exposed are shown to successfully mutate. The "virus" is found to be a spreadable corruption of genetic material, which causes rapid mutation in infected individuals. All large animal life above ground is soon infected.

January 1, 2040: 98% of all animals in Japan are wiped out, ecosystems ruled entirely by infected individuals.

May 8, 2048: Japanese Defense Force engages infected individuals to preserve quarantine. Coordinated attacks by infected humans and animals are seen. High levels of intelligence confirmed.

May 10, 2048: They fail, and the nation of Japan ceases to exist.

October 13, 2048: The United States Carrier George W. Bush is attacked and sunk by an unknown force. Later revealed to be a coordinated assault by the infected. Use of atomic weapons to destroy all life on Japan considered, but denied.

February 12, 2052: Remaining inhabitants of Japan have appeared, by outward observers, to begin adopting the infected into their religions. Part of this religion is a total weapons bad, and the banning of violence against infected individuals. This is surprisingly effective at ceasing conflict with infected individuals.

April 2, 2055: Infected seen to have spread to North America. Military preparedness results in a far more contained infection. Hundreds of thousands in the United States, Canada, and Mexico die.

March 11, 2061: The United States Army begins experimenting with the combat prowess of infected animals, which are shown to have a friendly connection to humans who treat them well, much like dogs. Initial tests exceed expectations. Later that same year, China, Russia, Vietnam, and N. Korea react by signing the Kommu Pact, ensuring protection against the now utterly overpowered West.

July 2, 2063: The Kommu alliance declares war on the United States. Infected used to great effect.

November 9, 2066: War end. Communist states dissolved, China and Russia (and all of Asia) are now under the jurisdiction of the NATO.

December 25, 2072: The regions, now divided, that were once Japan begin to open up to the outside world. Mostly through scientific trade off.

February 1, 2081: Japanese scientists sneak into heavily infected Brazil. They recover the DNA of one of the individuals believed to be one of the first infected.

Beliefs are that the infected are actually the next phase in evolution, and to find one of the originals would better help the understanding. There are many tried and failed cloning attempts, before a final experiment is successful. The result of this experiment, capable of self-induced Energy-Matter transference, is responsible for the deaths of dozens before escaping.

May 22, 2081: Ash Ketchum turns 10 years old."

As you can see, there is a heavy fanbase for this (ehhhh... sorta) "pre-game war" idea, and many poeople support it. Of course, this is only Part 1 of my Pokémon Conspiracies story.