A character pretending to be something she isn't is actually pretty common in RPGs in general -- I have a warlock who has the Charlatan background and pretends to be a cleric of Waukeen (the Pact of the Tome helps a lot here). Even her table-tent uses her Charlatan identity rather than her 'real' identity. I've also got a Chaotic Good cleric who doesn't realize that she's a Chosen of Cyric -- she doesn't know enough about divine spellcasting to understand that none of the holy symbols she carries save one are actually potent -- she only knows that for certain spells, she has to use the one with the skull in the sun or the spell doesn't work.
More problematic is the concept of 'I'm joining a faction so that I can secretly work to destroy it from within'. Suffice it to say that the good factions don't let evil characters join for precisely that reason, and the factions that do allow evil characters are experienced enough that they'd already have policies and procedures in place to be on the lookout for potential 'moles'. As noted above, if you're OK playing a character who will never actually get to achieve her goals in that regard, then go for it, but the moment you decide to actually start playing toward achieving that goal, you're probably going to fall foul of the rules about disruptive play in AL. Be warned.
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Pauper
More problematic is the concept of 'I'm joining a faction so that I can secretly work to destroy it from within'. Suffice it to say that the good factions don't let evil characters join for precisely that reason, and the factions that do allow evil characters are experienced enough that they'd already have policies and procedures in place to be on the lookout for potential 'moles'. As noted above, if you're OK playing a character who will never actually get to achieve her goals in that regard, then go for it, but the moment you decide to actually start playing toward achieving that goal, you're probably going to fall foul of the rules about disruptive play in AL. Be warned.
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Pauper