The original plot would have delved into the mystery of how the world came to be inhabited by Pokémon and what happened to the real world animals that once existed in the past. This would have been explored through the discovery of a fossil in the Pokémon world; the fossil of a real world tyrannosaurus rex. The fossil would be restored back to life, leading to the creature going on a rampage across the Kanto region. The anime's main protagonists, Ash, his Pikachu, Brock and Misty, and even the shows main antagonists, Team Rocket, would have spent the movie bringing the dinosaurs rampage to an end.
Shudou spent half a year devising this particular plot, which was shot down by the producers under the reason that "A story where a bunch of minerals gain consciousness and comes to life won't be a hit".