It does fit the plot, as it's a chronicle of spirits, as it were. There may be some games out there with 'spirit' or 'chronicles' in them, although I don't know of one with both. We're making a completely different kind of Pokemon game, which is why we immediately decided against anything color or gem related. Personally, I like the name better than any of the alternatives we thought of while brainstorming.
Also, I think it sounds pretty cool, at least compared to some of the other fangame names I've seen.