Originally the movie looked nothing like this...
The Third Pokémon Movie, released in Japan in 2000, originally had a completely different plot to the version released. The original plot existed in an early first draft written by Takeshi Shudou (main writer of the anime series up to that point as well as the first two movies). This original script was apparently auctioned off for one billion yen (the equivalent to around 8 million US dollars) to a buyer who went only by the name of "Suu". The location of the seller, as well as whether or not they still possess the script is unknown.
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 forementioned 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".