We have fairies on my online game. Well, two different online games that I played.
For starters in the first one, in Final Fantasy XI, in the game's story, way before the current timeline with the war that had happened, fairies used to roam the lands. A lot of the humanoid monsters, the beastmen, had trapped and killed the fairies in the past, making the fairies absent in the current timeline. However with the 4th expansion pack, Wings of the Goddess, you can travel into the past (the story is complicated; you'd have to read about it yourself) during the Crystal War and free the fairies. You fight and slaw the beastmen, and they drop the bottles that the fairies are in. If you release a lot of fairies in an area, they will appear in the current timeline! However, it is very WRONG to have you, as a player, kill the fairies by accident. See if they appear in the current timeline and you are trying to get stronger in an area, the fairies will heal you so that you are at full health and not sick with status ailments
In the second Final Fantasy MMO, Final Fantasy XIV, fairies are apart of the lore for the Scholar job. You can summon them in battle and they can heal you and your teammates, as well as giving you increased attack speed, magic defense, and spell speed. The 2 fairies we have are named Eos (the healing fairy) and Selene (the support fairy); both of them can heal you if you take damage, however they do defer in their abilities. Both Eos and Selene are actually a fair that has been split into two forms! Combined, their true name is Lily. You would have to play the game to actually know the story behind the Scholar job, as well as its origin in the Floating City of Nym.
http://finalfantasy.wikia.com/wiki/Faerie