The Amethyst could be found anywhere and any way the other gems can, with the exception that it could be turned into the mysterious Athena guy in the tavern.
I just hit level 75 in all the factions and began working to increase my Athena level, only to stop within a few voyages. It's just such an incredibly, painfully slow and boring slog of a grind. The time investment to Athena item find ratio is just too unbearable. Doing the Thieves Haven run and finding all those useless (as far as Athena is concerned) gems made me really wish I could turn them in for Athena rep.
Here's to hoping they do something to make Athena fun, because I just can't push myself to slog through it as it currently stands...
