As an AI language model, I can help you with the initial structure and ideas for your game. However, building a complete game with 1000+ Pokémon, complex systems, and plot twists solely within the constraints of a single HTML file might be a challenging task.
Here is a basic outline to get you started:
Please note that the code provided above is just a starting point and you will need to add your actual game logic, data, and visuals. It is highly recommended to structure your code in separate JavaScript files and link them in the HTML if the game becomes more complex.
Building a comprehensive game with numerous features, plot twists, and a large number of Pokémon will require significant effort and expertise in game development. You may need to consider using more advanced frameworks or libraries to aid in development.
Remember to consult appropriate resources and references while programming your game to make it enjoyable, engaging, and heartouching for the players. Good luck with your game development!