Also, because of this war is why there are so many wild Poison type pokemon.

Ditto is a failed Mewtwo experiment, remember how Mew has every other pokemon’s DNA, well, that’s why Ditto can transform into any pokemon.

Porygon is an attempt to make a war machine using the aid of pokemons.

You are assigned to rebuild the pokedex’s database, because during war all data on pokemon was loss.

the war will start at 2012, that’s why only after the war the Pokemon will populate the earth. The Pokemon of legends are false memories implanted by the government to control the remaining population. 

Giovanni realized that hence he started this “Evil Organization” to liberate each one of these “Pocket Monsters” brain controlling creatures sent by the United Nations.