One day, a Gulpin was rolling around underneath the bicycle path in Hoenn, when the crazy old lady on the route accidently whazoced it with her walking stick. The poor poison Pokemon was sent hurtling all the way down route 103 till it splashed into the water.
After many days of helpless floating, the Gulpin saw a huge shadow underneath, desperately struggling, it realised the shadow was getting bigger and bigger, untill..
SPLASHCHOMP! The gulpin was devoured by a Wailmer.
The Gulpin however, was not digested, and gave the Wailmer a strange stomach disease.
The Wailmer was later caught by a trainer who force fed it Rare Candies that were several months past their sell by date, forcing it to evolve into a Wailord.
Upon evolution, the Gulpin was fused with many internal organs, already mutated via the disease, and slowly morphed into a living gall bladder type apendage.
The Wailord started gagging, and, much to the trainers surprise, threw up a strange blue mutent thing covered in Wailord juice.
The trainer kicked it into the rapids and carried on his way to find some secret cave or something.
In the swirling undercurrents of the rapid moving water, the grotesque blue organ mutant was thrown about violently, slamming into rocks and all sorts before eventually washing up on Dewford Island.
Brawly found the strange thing and decided to inflate it... by a means too horrifying to discuss, but it is safe to say he used it as a punchbag for several months.
Eventually, Mr Briony arrived in Dewford, his beloved wingull spotting the organ-mutant-punchbag that Brawly had tied outside to a pole for some reason, probably dipping it in paint to re-paint the gym, and swooped down to peck at it, pulling tangled bits of mutant flesh off with it's beak. Eventually it pulled it off the pole, and flew high above the clouds and far away whilst Mr Briony and Brawly discussed... something...
However the wingull was attacked by a Swellow, causing it to drop the bladder-esque thing far below itself, where it violently slammed against rocks as it rolled down a mountain and into meteor falls.
The deflated,battered,raggy mutant organ balloon thing floated helplessly on the water, barely alive, untill it was caught in the middle of a fight between a Solrock and a Lunatone, their respective psychic blasts both hit the thing at the exact same time triggering some odd mutation, again, to create a being unlike any other.
This is how Manafi came to be.
Fione is simply a brain cell mutation, like a tumour, that Manafi gets rid of by expelling it's brains, letting fish eat Fione off, then swallowing it's brains again.