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Location: Australis - Based on south part of South America (Argentina, Chile, Bolivia, Peru, Uruguay and Paraguay)
In one version you're the typical 10-year old trainer that is given a starter by a local researcher.
In the other you're a 56-year old man in a quest to find the thrill of being young in his/her new adventure.
In each version, the character from the other acts like a friendly rival.
Team Mindcrime's intention seeks to having direct control over people's minds to establish a new world order. At first they try to do so by terrorize people, making Pokemon suffer publicly.
While people feels unprotected from this threat, a new team called Team Saber appears, made and funded by Silph Co, formed mostly by upset citizens, and their leader, Dr. X, who, incidentally, is the league champion too.
Our character joins this team and manages to, somehow, ruin Team Mindcrime's plans. Soon your character watches a cutscene where he/she realizes everything. Team Mindcrime was also part of Silph Co. plan to earn the trust an power from people.
Naturally, you and your rival being the only ones that know, go to overthrow Team Saber too. Team Saber has the trust of everyone in the region, and because of this, and Silph Co's campaign to make you the most wanted person in the region, you're treated like shit by the NPCs. You're now a threat for peace.
When you go to challenge Elite Four, they seek to arrest you. Finally Dr. X challenges you and tells you he's sick of all that shit.
The plot concludes with Looker sidequest, where you manage to dissolve Team Saber with help from him, Dr. X and your rival. You find enough evidence against Silph Co. The final cutscene of the sidequest shows Silph Co. president going free and mocking at you on how he used his money to bribe everyone in the trial.
After the Looker sidequest, NPCs stop treating you like shit though.