no there is no story to them but i just make up my own.

e.g- the Dark Aeons are Spiras strongest Fayth, controlled by Yevon,s high council who actively seek you out when they realise you threaten there rule.

Penance is Beville,s strongest Machina who was the main instrement in the destruction of Zanerkand 1000 years prior. he was defeated by Sin.

however even Sin could not destroy it. it was bound in the calm lands by some kind of magic spell by Yu yevon. however, the spirits of the dead dark aeons break this seal and unleash it.

it has long since lost control and is just as dangerous as SIN. and if they fought again, the likely outcome would have been Armageddon.