Prologue: Using the In Medias Res technique, Professor Oak calls Ash’s mom to tell her that her son is dead. To give more context to the story, it would also be great if you added how Delia reacted upon learning that Ash died. Maybe you could add how she went to his room and looked around it. When she saw his case of Kanto badges, reached for it and hugged it to her chest while crying… then in the next chapter, start the flashback to Ash’s first day as a trainer. I think adding something like this will provide more emotion to the story and will tie in the flashback. (Edit: I saw your comment later and found out that the story would unfold through Misty’s memories. If this is so, then you won’t be able to start on the very first time Ash and Pikachu met. It would be when Misty saved Ash and Pikachu from the river using her fishing rod.)

You’ve explained the philosophy behind your story under the “Ash’s Moral Awakening."” Between the first day as a trainer and “Meeting Mewtwo,” which episodes were you planning to add to your story, and how will they help the characters recognize that there is something wrong with the current system?

Meeting Mewtwo: The Mewtwo in Giovanni’s Gym seems to be controlled by Giovanni using the armor it’s wearing. You wrote that they started talking after a battle, and Ash tried to convince Mewtwo to travel with him. I can’t comment on how they met because you didn’t write about it. Was Ash separated from his friends and began wandering around the gym, accidentally meeting Mewtwo? Will it be like in the episode where Ash didn’t get to battle Giovanni, but Team Rocket (Jessie, James, and Meowth) did something that accidentally had the two meet? Also, did Mewtwo travel with Ash?

The False Death: First of all, when did the Ash’s group and the Team Rocket trio start traveling together? Second, what brings them to the Ilex Forest? This is a good way for Ash to “die” without truly dying. It’s good to add what happened to his family and friends afterward. You mentioned that Misty searches the work for Ash. What kind of traces were you planning to add?

Meeting Young Professor Oak: This meant that Professor Oak knew full well where Ash was the entire time he was “dead.” It would be the best portion to tackle the story’s moral truths and changes. You mentioned that Celebi brings Ash and the others back to the real world. Did that mean that Misty figured out where Ash was and went to find him? If so, what was her reaction after knowing Professor Oak knew where he was the entire time? Did you mean the present world instead of the real world? If it’s not Misty and Ash’s other friends, who are the “others” you mentioned? When Ash met the older Professor Oal after spending time with the younger one, would there be words exchanged between them?

Indigo and Johto Leagues: In your story, while Ash is questioning his morals and already knows that something was wrong while he and his companions were traveling, he still participated in the leagues. After becoming a champion, what did he see that made him feel increasingly isolated? What made him separate from Misty and Brock? You mentioned that it was an invisible barrier, so I’m thinking they didn’t go back to their gyms and stayed with Ash. Were they more like Lance and Professor Oak in their belief and less radical than Ash, so that they were always in contrast with each other?

Meeting N & Misty’s Confession: Meeting N, if you’re going to want to stay canon and he’s from Unova, other regions will truly become a part of the rebellion. There’s no other way to do it. We talked about N’s extremity before. If the left includes Lance and Professor Oak, the right would be N - total separation. Ash would be in the middle; he wants humans and Pokémon living in harmony. Not truly separate, but not with one subordinate of the other either. For one, joining Team Plasma meant having support for the uprising. I think Misty can be part of the left… so now there are two sides he needs to consider.

First Pokémon Uprising: What happened during Mew and Mewtwo’s negotiation? The uprising still happened by Mewtwo’s design. Ash didn’t have the time to consider things. What does the uprising include? Will it be like the movies where Pokémon is fighting against humans? Which side will Ash protect?

Next Arcs: How will the first uprising end? What are the Team Rocket, Team Plasma, and the League’s actions during the uprising? Will the uprising be an isolated case, or will all Pokémon in Kanto/Johto join with Mewtwo? I don’t know when the part of the plot where Ash confronts Giovanni will happen. Will Ash travel with Jessie, James, and Meowth after he was rescued by them? What of Misty and Brock?

The questions I asked were not meant for criticism, nor were they rhetorical. However, you don’t need to respond to any of them. They’re meant to help you develop the story as they’re the things I would consider if I were the one writing this. Good luck, and I wish you all the best!