Runes are items in the game that can be used to enchant weaponry with the power of alignment. There are 4 runes in the game: Air, Earth, Water and Fire.
Each of these can be found by any creature of the same alignment. For example, if you are fighting a creature with Air alignment, there is a chance it will drop an Air Rune.
There are 4 boss creatures in the game that can drop runes as well. Not enough information is known on the bosses, as they are researched they will be updated.
Finally, to enchant a weapon with a Rune, you need to be the current alignment in game. If you want to enchant an Earth rune into a weapon, you need to be Earth alignment yourself. When you have met the requirements, visit the appropriate shrine in town to upgrade your weapon.