Backstory: 50 years ago, aliens come to earth. hey attack Asia, but japans military drives them out. Remains are sent to a museum in Tokyo Present Day: Jack, the main character, goes on a field trip to japan with his classmates. He goes to the alien museum, for his school project.
Greninja, Beedrill, and Nihilego
Deigo, Jack's Classmate
When Jack gets to the museum, something goes wrong. There is a robbery and Jack sees a figure, Ash Ketchum. Ash steals alien tech and unleashes an army of Pokemon to do his bidding. Some of the tech is left behind and Jack takes a sample for himself. The evil Pokemon destroy japan and go to attack the rest of the world. Jack is stranded in japan and plots against Ash.
Jack and his friend Diego (the genius) figure out how to make a Pokemon army of his own. He remembers them as he childhood card game he played when he was a kid. He only has a limited amount of alien power so he chooses his army carefully. With the help of his friend Diego, the two train the Pokemon in order to ready the fight against Ash. Ash sees the training and puts it to a stop. He attacks Jack and warned him not to get in his way, Jack was badly hurt.
Nuke Protocol: READY
Jack leads his team of Pokemon to Ash's factory base in Tokyo. On the way they battle Pokemon and win all the battles. They encounter Ash and beat him in a fight. They defeat all of the bad Pokemon and Ash escapes to his laboratory base also in Tokyo.
At Ash's lab they have another fight goes on, between Ash's and Jack's remaining Pokemon. During the fight Jack destroys Ash's machine and it starts to make the Pokemon disappear. Ash is trapped inside with some of his remaining alien tech. Jack cannot defeat him or bring him to justice, due to a giant fire. Jack escapes and Diego starts Plan B.
As Jack escapes (on Charizard's back), Charizard starts to fade away. Jack drops into the North Pacific Ocean. Meanwhile at a military base in Honshu, Diego prepares for Plan B. To nuke/bomb Tokyo. With the military codes from General Hux, Diego activates the bombs. A scientist, Professor Oak, finds the wright hacking codes for Diego. Just as Jack plunges into the ocean, Diego launches the bombs. Tokyo is a crater and all around is dust. Ash's body was never found.