Attention fans of this fanfic. I am sorry to say I have lost interest in writing this fanfic. It is because I believe there are just too many mistakes on my part in which I would have to completely rewrite the story from scratch. So to all my loyal fans, here is the summary of what I had planned to happen if I continued writing this story.
I was going to reveal that Ash's father didn't die during a mission, but it was May's father who killed him as a way to prevent him revealing the truth about the Team Rocket Organization, as he believe that would cause more destruction and chaos from the order it brought. He pleads that he is sorry, and helps the group get through Team Rocket's defenses through a network of secret tunnels. One by one the group needs to separate to get the plan to work.
During this time, it is revealed that Team Rocket has been lying in wait for the Elite, and easily overpowers the group and takes down the Elite HQ. Domino aka Tulip is a double agent and holds a gun to Mewtwo's head, stating he shouldn't have stopped reading minds or he would have seen this coming, before shooting him. As well as Gary aiming a gun at his grandfather, the scene cuts out after that.
Then, Ash meets face to face with Giovanni, where it is revealed that Giovanni is actually Ash's uncle and his father's brother. He gives the idea to Ash that they could rule the world together, and reveals what Team Rocket has been doing for the past 200 years.
However, he doesn't realize that all he has said has been broadcasted all over the city on the emergency network thanks to the help of Ash's friends, causing a massive revolt. During this distraction, Ash is able to make it to the machine and implant the devise, causing a blackout in the city, shutting down the barrier and a burst of energy to cover the planet, recovering all of the Pokemon.
I have the story jump a year later, where humans and Pokemon are living together in harmony, and Ash and his friends get ready to go on their Pokemon Journey. Ash however forgot to pick up the Pokemon from Professor Oak and rushes to the lab to find all of them are already gone. Misty, now girlfriend, yells at him for being so absent minded. But Oak mentions that he just remembered he has one more left.
Oak gives him the pokeball, a to Ash's displeasure, is the Pikachu from the Elite Base, though after Misty picks him up, Ash goes to touch the Pokemon, only to be shocked with a thunderbolt.
And that's how I was going to end the story. I apologize once again for not being able to finish this story properly.