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The antagonist will be
The Master. After crashing the TARDIS on this fascinating planet he/she learn that he plans to enslave the entire Pokémon world and all its inhabitants by using the power of Kyuurem. And it is up to the protagonist, aka the Doctor, to stop him. The only way to do that is to beat him in a battle which means that you'll have to beat the Gym Leaders and Elite Four (who are unaware of his plans) because he happens to be the current league champion. He/She will not have an assistant because the Pokémon he/she amasses over the course of the game will be the assistants.
What? This is Wild Mass Guessing after all.
Guessing the Master is not that Wild