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So, I'd like to be in either the Pheonix or Aurorlock Allegiances, and I know that you have to buy the prefix off of the store, but isn't there something else that you have to do? I'm really confused about the entire process.
You can buy the Aurorlock Phoenix prefixes off the store, or either of the packages. There's nothing else you necessarily have to do, just be in game while you make the purchase to be sure it goes through. If it does go through, you'll receive a message in game that goes along the lines of "You have successfully bought (item)!"
So, I have to be in the game as I'm making the purchase, otherwise I won't become a member of the specific Allegiance that I bought, correct? And does this go with S.P.E.W and Werewolves, too?
It technically isn't required to be in-game when you purchase a store item, however it's recommended as being offline at the time can sometimes cause issues with the purchase. And yes, it's the same with club packages like SPEW and werewolves!