First, there's some more hidden stuff to find in the previous areas by using Surf and Strength. There's some nameless old guy looking for a legendary pokemon in a cave near Mistralton City. When you find him you get a bunch of unexpected backstory involving the origin of pokemon.
I see you're quite skillful for your age... Perhaps you could... hrm... It's a possibility, I suppose... Well? Will you lend your ears to this old man's ancient story?
It was long ago, when people and Pokémon lived in their own separate worlds... Through a war humans started, a forest in which Pokémon lived was engulfed in flames.
The Pokémon could not escape through the fire and smoke... There then appeared the legendary Cobalion, Terrakion, and Virizion! Terrakion used its characteristic strength to destroy the boulders blocking escape. Virizion made use of its swiftness to protect Pokémon from the sparks. And Cobalion guided the frightened Pokémon out of the forest.
Cobalion, Terrakion, and Virizion fought away the warring parties with overwhelming strength. The parties, frightful of the power the three showed, at last put an end to their war...
If people do not cease fighting, Pokémon can have no peace. The trio knew that people's deeds could cause the loss of many lives... To avoid contact with people, they went away to places unknown... Since then, the three have almost never been seen, and they thus turned to legend...
I have been searching for them for countless years on end... And at last, I have ascertained there to be one deep in this cave. But the legendary trio has no trust in humans. If a person draws near, they will bare their fangs and attack. They only know the world as it was so long ago, so it cannot be helped... They remain ignorant of the fact that our world has become one of people and Pokémon understanding and helping each other.
Perhaps if you could make them realize that people and Pokémon can live together in trust... Even they could choose to live with people if given a reason to reconsider them...
Who knew pokemon could be this deep? I feel like I'm reading Princess Mononoke... stuff about humans and intelligent forest creatures at war with each other...