Life was once perfect. The humans, the environment, and Pokemon were in perfect balance. Sure, many tried to tip the balance one way or another, but brave trainers always righted it. At least, as much as they could...Too many imbalances took the Surface from us.
Something went wrong with the Legendary pokemon. They came out of hiding and fought with everyone. Trainers, wild pokemon, even people without any pokemon fell to their angry attacks. The bravest of trainers investigated every possible lead--old Team Rocket tricks, the newer but still deadly Team Plasma, and imbalances with our neighboring dimensions. But, they found no conclusive evidence for any of their ideas. Finally, they decided to team up and take down the legendaries once and for all.
That was a huge mistake. Yes, every legendary was killed, and they could no longer attack us humans, but the balance of life was permanently tipped in the humans favor. Soon the weather grew out of control. People became sluggish, depressed shells of their former emotions. Wild pokemon violently attacked humans and pokemon alike. It became dangerous to go outside, so many stockpiled all the supplies they could get and holed up in their homes. Finally the government issued an emergency evacuation from the surface. A sandstorm as big as the Red Spot on Jupiter was due to hit Kanto in five days, and nobody could breathe in that. So, the government poured all of its money and resources into the Magnet Train line. Those subways stretch over every region, and can hold over three hundred thousand people. With everyones stored supplies and the governments money, the population of every region could live there. And, we did! For thirty-five years we lived there.
And now, in Station 5, or Neo Saffron, the first Station-raised generation is ready to go to the surface. Most trainers like to make their Journey around the surface, scrounging for supplies, rare pokemon, and any treasures left, before they return to the station and officially start their life as an adult. Trainers have to be fiveteen to get their license, as wild pokemon are stronger than before, and life can be brutal on the Surface. Only experienced trainers who were old enough to remember life Before the Sandstorm have gone up now. They say Nature is still brutal, and the legendaries are still gone. There are bandits, angry wild pokemon, and crazy storms. But, there are also supplies left free for the taking, migrating tribes, and traveling merchants with all sorts of rarities, like chocolate and pokemon eggs. It's a true adventure just waiting for us to experience it!
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Okay, here's the first post/plot summary/whatever I used on another website. The basic idea is that each character gets a legendary egg (from a list of legendaries that have to do with nature. Sorry, no Genesect.) that will hatch much farther on in the series. We're all new trainers with one pokemon, five extra pokeballs, and a pokedex. (Unless you're from the Surface, in which case you'll have to loot supplies or trade for them with the travelling merchants.) On the way to getting/hatching the eggs, we will fight wild, aggressive pokemon, bandits, Team Rocket (I'm planning to have them be a focal point in the plot), and do the regular "catch pokemon, battle for badges, etc."
I want this to be a more serious Pokemon. Pokemon will get hurt, trainers will be attacked as well, there may be serious injuries, etc. The worst thing that can happen is not a fainted pokemon, but a dead one.
I have a lot more ideas, too, but they're mainly details. Interested?