What happens when the son of Death and War is trained as a Warrior to serve as a tool in his Mother's quest for revenge?

So I'm sure most of you noticed the 'Pokemon Tower' in Pokemon Red (or whatever version you played), and the creepy, haunting feeling it has. Then how in Pokemon Silver, Gold, and Crystal, the Pokemon Tower is replaced with the Radio Tower. Apparently 'Rest In Peace' doesn't affect them at all...just imagine an entire cemetery, where the dead were buried, tomestones everywhere, families and friends visiting their loved ones, all wiped out like it was nothing... [Rated PG-13 just to be safe]