The story takes place in the Future (in the year 2124). You play as a boy/girl (or with edited sprite as man/women) and you work as a space pilot. The energy sources on earth have been exploited and people are now looking for other energy sources on the moon. In the year 2104 Scientists dicovered black stones, on the moon, which contain dark energy in concentrated form , also called Turner-stones (as a tribute to Turner, who coined the term dark enery). Your grandpa, (Prof. Oak) (here scientist and in charge of the space travel mission) studies the Turner-stones and his mission is to exploit the energy of the stones. The Turner-stones seem to emit some kind of wierd radiation but you grandpa tells you that he manged to proof that it isn't dangerous.
You start off in your home town (of cause edited) and your grandpa sends you to a space mission to explore a Turner-stone source. The world is governed by one all powerfull government which has a very severy policy (because of the energy-crisis the crime rate expanded rapidly and the government does everything to maintain order). Than after a little chat with your grandpa (to explain the background story etc.), you go to a space training station and have to collect your space-pass. Then you are allowed to fly to the moon. New technology brought up a space-phone and the astronauts can stay in contact with earth. There is an artificial nature section on the shuttle because scientists also try to find out if closed environements could survive in space in view of civilizing the moon. When you arrive on the moon you get a call from your grandpa and he tells you that the radiation of the Turner-stones has severe effets on animals which he didn't predit. All animals exposed to the Turner-stones mutated and became very big. Afterwards they attacked humans and sort of "poked" them and it seemed that they sucked by the people's body... the government announced code red in the city ...... Then the connection breaks off. You remember that the scientists brought along animals to the moon in the artificial nature section and leave your room to take a look. You hear strange noises from the artificial nature room but can't enter the room. Then you go on to the main section and listen to a conversation between the government and their police on the shuttle. The town in which your grandpa lives should be "put apart" and they get the mission to kill everyone which had contact with the Turner-stones.
On the Moon:
The government-police men put on their radiation suit and leave the room on the other side. You can't exit the room before you find Charile, grandpa's dog, which travelled along. You ask yourself why the dog isn't in the artificial nature room and wonder why he isn't affected by the radiation, then decide to take him with you as protection (here you obtain your first pokemon it could be Arcanine or some other pokemon dog). The government police shut down the energy supply and you can now enter the artificial nature room where have to fight your way through. Here you find a lot of dead bodies and also the first ghost (which you cannot fight yet). The mutated animals absorb the bodies of humans but someway their souls remain (they emit the same force as the Turner-stones). You remember that there is another space shuttle (its mission is to look for habitats on the moon) in reach, but it would be too long to get there by feet. You must obtain a hovercar (pokemon sprite/pokemon which can use surf) and find the hoverkeys (badge you need to use surf). After you go outside you remark that the shuttle is completely destroyed and that the animals managed to escape. You have to fight your way through (outside the battle pokemon sprite should replace trainer sprite and inside the battle the trainer sending out his pokemon to the fight shouldn't be visible). As you reach the new shuttle you have a beat the security (this time, inside the battle, a trainer sprite should replace the pokemon sprite and the trainer sending out the pokemon shouldn't be visible). Then you go to the cockpit of the shuttle and beat the pilot down and fly home.
In the Wasteland:
Here I only have a few rough ideas: When you arrive home, you crash the shuttle and find your vilage completely destroyed. The government has bombed the city with an atom bomb but this couldn't get rid of the ghosts. You enter grandpas's house and find a machinery which he used to trap the energy of the Turner-stones. Now you can beat ghosts and trap them in this device. (NPC disappear after you beat them) Ghots are everywhere and they can control pokemons (the mutated animals), but not only ghots await you but also radiated people who (like ghosts) work together with the pokemons. You will find a lot a messages written by a person who calls himself "The Lurker". He gives explations and seems to be the only survivor. (he also defines the name:"pokemon"/poking animals from the moon). In the game there shouldn't be too much pokeballs around, you rather have to defeat pokemon sprites to get pokemon. "The Lurker" explains to you that after beating the wild pokemon they will become domestic but he hasn't found a method to keep them on his side. Here the machinery of grandpa comes in handy you use it to store up to 6 pokemon, the rest is saved to a chip. You can modify the accessible pokemons by connecting to a pc, but therefore you have to repair the pc's first. In pokemon centers you will find first aid kids. Your quest is it to make it through the city alive and escape the government which wants your death, but be warned about radiated people, the pokemon and the government police which tries to get you and bring you down. AND BEWARE OF THE GHOSTS STRIVING FOR REDEMPTION!
To save the world and get rid of the pokemon, you travel back to the moon (the origin of the bad) where you have to beat the 4 guardians (pkm league) and bring back the world to peace. There you meet Arceus (pkm champ) and you have to proof yourself to him and perhaps he brings peace to the world after you beat him?
Good idea or bad idea? New ideas are always welcome