I've been working on writing out a story for a Ninja themed Pokemon game. "Pokemon Hidden Village"
The Location is a small the small island of Tokanjo which is the home a community of people who live there a help run the port, the inn, the market and the farm. In the center of the island, guarded with a thick jungle and lots of exotic poke lies the Hidden Ninja Village of Tokanjo.
The ninja protect the island from would be pirates and criminals, and they also seek just for pokemon cruelty and offer their jungle as a refuge for pokemon that have been abused.
The main character is a young boy or girl who grew up in the port village and had only ever heard of the rumors of the hidden village at the islands center.
Initially everyone starts with a special nincada, which you find at the bottom of a hole in a cave when the game opens. The nincada had been raised by the ninja and was lost once during a mission.
Upon returning the the village you arrive just in time to stop pirates from attacking. Little did you know the Tokanjo ninja were already on it but the sensei takes notice of your bravery and sees you battle it out with pirate grunts. Upon the Pirate Captain challenging you the Ninja Leader emerges and the two of you double battle against the Captain. The captain greatly out levels you but the Sensei and his Accelgor greatly out numbers him. The sensei then asks you to join the ninja and offers you the first of your ninja starters (chimchar, froakie, rowlette) Eventually you get all three but you will trade him the nincada you found for the first of them.
Upon receiving this pokemon you've been awarded a head band to represent your status as a Genin of the Tokanjo Ninja
Each Starter has a different master in the academy that will give you missions on the island and let you battle them. Once you've fully evolved the starter you can challenge the master and once you beat him you will receive your next starter.
In the part of the game as a Genin, you are only permitted to carry once pokemon at a time so to advance your island missions fom your second and third starters you must deposit your other in the pc.
Once you've evolved all three starters and defeated the third master you are officially promoted to be a Chunin and you can now use a three pokemon team
Next you get offered a main land mission where you travel to Kanto to stop witches from covering the whole regions pokemon population into ghost pokemon
Upon returning to Tokanjo you once again find the pirates attacking the island, this time with a lot more power and this time they have discovered the hidden village. You battle the captain but even after defeating him he seems to be over powering you, just then the sensei accelgor gives you an egg and tells you you've grown strong and to continue to grow and protect pokemon and our home. It uses final gambit and defeats all the enemies but sadly dies. The sensei in light of loosing his strongest pokemon promotes you to the position of Jonin, You now have the egg of shelmet which you can hatch an immediately evolve without all the trade nonsense
There are defiantly other pokemon i would like to make avail be through events.(Zubat, Sneasel, Zorark, etc) I think that every pokemon you get will be through events in this game. I would also like to focus on unique ninja times that like a ninja belt that allows you to stack 2-3 items on one pokemon. Items that will make non poison moves cause poison would be cool.
The final part of the game will be a battle against Deoxys, an evil organization have summoned it and and failing miserable at controlling it and are making it wreck havoc. Once you completed this final mission you are promoted to the level of Sennin and even though you have the badges you are permitted to challenge the Kanto Elite for to bring Honor to you people who have saved the world.