Why do you not have a father in Pokémon games? Where is your rivals Father? You know, there was a War in Pokémon long ago...
In the English releases Red and Blue, Surge says "Electric Pokemon saved me during the war." and that the player wouldn't last in combat. This is a key fact from the games that supports the theory. The theory states that the was a war before the events of Red/Blue. Notice a significant lack of adult men in Kanto? Especially your own father, as well as Blue's father? The theory states that the men are all gone because they died in battle. All the adult men in Kanto are either in organised crime, or are Gym Leaders (or both, like Giovanni), so they would not be needed to go to war, as they have Gym duties, or get out of it by their mafia status. In Kanto, there is also a significant lack of entertainment venues (cinemas, theaters, arcades etc.), and religious/ cultural buildings (synagogues, churches, temples etc.). They were destroyed in the war, even that one spot in Vermillion City that the man and his Machop are rebuilding. More buildings were most likely destroyed, even Gyms and Pokemon Centers, but were rebuilt first due to those being higher priorities than entertainment. That's the basic theory, and many fans have their own theories that add on top of this. This next part is my theory of what might have happened. This is just my theory, and I'm not saying it's true, just saying that it's plausible. Okay, in the Japanese versions of Red and Green, Lt. Surge is referred to as "The Lightning American". American.
Now, in the Pokemon universe, the closest we are going to get to America is Unova, which is based on New York. So, putting two and two together, we can say that Lt. Surge is from Unova. This means that the war would be between Kanto and Unova, or Japan and America.
In Black/White, and Black 2/White 2, Ghetsis is seen in a large robe, and with a single lens covering his right eye. The robe is draped over his right shoulder, and conceals the entire right side of his body. In the intro to Black/White, when Ghetsis is crowning N as Team Plasma's king, his right arm can be seen blackened, and in his VS sprite in Black 2/White 2 shows his right hand is bandaged. It's safe to say that since his arm is blackened and bandaged, that some sort of fire or explosion that injured him. Some reasons a war breaks out is a conflict of ideals, or to stop a threat to humanity. Let's explore these in terms of the Pokemon games. What are Team Rocket trying to do? Enslave or exploit Pokemon. And Team Plasma? Liberate Pokemon and set them free from humans. There's a definite conflict of ideals there. This is a minor factor however, as organised crime groups don't have much influence on government, but the government may have seen this and intervened.
The global threat? Well, I think that bringing Mewtwo into the world is a huge threat to Earth, as we saw in the movie. And Team Rocket was working out of Pokemon Mansion on Cinnabar Island when Mewtwo was born (not cloned like in the movie, according to the diaries found in Pokemon Mansion). Mewtwo went crazy and then blew up. It can be assumed that Unova's armed forces were in Kanto at the time, hearing of Mewtwo and trying to stop it. Ghetsis was also a soldier, and was on Cinnabar Island when the Pokemon Mansion exploded, burning his right side.
The explosion is seen as an act of war against Unova, and war breaks out. Enter Kanto's armed forces. Since Unova's people were in Kanto already, the battles are primarily fought in Kanto, and possibly Johto. Let's say that Black and White are set 16 years after Red/Blue (1996-2013). Now, judging by how far ahead in technology Unova is compared to Kanto, and seeing how that could not be simply because of the 16 year difference, it is safe to say that it is due to collateral damage from the war.
Collateral damage that was caused by a nuclear bomb. Just like America dropped a nuclear bomb on Japan in World War II, Unova dropped a bomb on Kanto in the Pokemon War. The nuclear radiation mutated living creatures, causing Pokemon like Grimer and Muk to exist.
Black and White state that there was a war in Unova, and a part of that caused a forest fire in which Cobalion, Virizion and Terrakion fought the fire and helped Pokemon in the forest. This is a strong piece of evidence that Unova was also in a war, and it makes sense that it would be the same one fought by Kanto.
Lt. Surge is American, but moved from Unova to Kanto to start a new life. Ghetsis, never forgetting his time in the war, unites Team Plasma, and remembering the scientific experiments on Pokemon from Cinnabar, works harder to liberate Pokemon. Kanto is still reeling from the events of the war. You and Blue are the first generation of peace in Kanto. Sailors are found all around, especially near Vermillion City, where there is a port, as they still feel as they need to defend their country, being a part of the Navy.