Complex sentence: He successfully captures Moltres, but the balance of power the birds have over the world's climate begins to collapse, causing all sorts of weather phenomena across the world, alerting countless Pokémon to the change.
Split into simpler sentences: He successfully captures Moltres, but this upsets the balance of power the birds have over the world's climate. Weather across the world begins to go haywire, alerting countless Pokémon to the change.