In the village hidden in the clouds at the end of the second shinobi war 

"Lord raikage! The storm is getting worse!" The third raikage grimaces and asks How bad is it? "At this point, the village may be destroyed!" Have we managed to discover the cause of this storm?

"There's a strange chakra coming from the middle of the storm sir!"

I'll move out then! The third raikage activates his lightning chakra cloak and vanishes, heading to the top of a mountain, where the storm is worse. What is that? The third raikage notices something strange at the very top of the mountain, there's a crib and the lightning is striking everywhere besides the crib.

A baby crib? The third raikage, approaches the crib and finds a dark skinned baby with glowing blue eyes inside. 

How odd! This baby has glowing eyes.. some kind of bloodline? Well, whatever let's get you out of here first. The third raikage instantly vanishes with the crib in arm, and speeds back to the village, noticing that the storm seems to have stopped after picking up the crib.  So, this child seems to have been the cause of the storm.. perfect for our kumogakure! The third Raikage A smiles at the thought of a potential strong ninja for the village, and he arrives back in the office where his assistant is waiting. Fetch me some baby milk! Although confused, his assistant quickly rushes to bring baby milk and returns after a moment. "Lord third, who's child is that?" I don't know, but the storm seems to have been caused by him. I'll adopt this child as my own! "What shall he be named?" His name shall be Raiden! My second son Raiden!