What's the story behind Shedinja?

in the main games, you get shedinja by evolving a nincada with an open space in your party, you get a shedinja in that next slot, essentially getting one extra pokemon as shedinja' s the discarded shell of nincada.

in the main games its gimmick is having 1 hp, but only being susceptible to super effective attacks, in a game like GO, they probably needed to make some special mechanics for it as types that dont effect pokemon in the main series are only treated as double resistance here and abilities are not present (Azumaril and Medicham wish they were)

MetagrossMaxis covered basically what is all about regarding it's unique mechanic in the main games.

Lore wise, it's basically an a possessed shell of a Nincada hence the ghost typing. That's the special story that it has. The main games and it's abilities are really what makes it interesting. In Pokemon Go it'll most likely just going to be a collector's pokemon unless they somehow add abilities (which I hope they don't. Go's biggest strength is it's simplicity)