Pokemon and Godzilla exist in the same world, but in different regions. The Pokemon region is where humans have learned to capture and train Pokemon using devices called Poke Balls. The Godzilla region is where humans have to deal with frequent Kaiju attacks using weapons and technology.

The connection between these two regions is that capturing Pokemon is actually a way of training children to fight Kaiju. The Poke Balls are based on a technology that was developed by studying Kaiju cells. The Pokemon battles are simulations of Kaiju fights. The Gym Leaders and Elite Four are elite trainers who have experience fighting Kaiju.

The purpose of this training program is to prepare the next generation of defenders against the Kaiju threat. The ultimate goal is to find the chosen one who can wield the legendary Master Ball, which can capture any creature, including Godzilla himself.