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I found it, it's a story called "Tales Of Attornia." Also, she did blow up a large populated area, except it was a city and not a town, and in an emotional state she levelled everything in the city, all because her sister died, an event that happens in the first game in canon, and this happens in the first chapter, her canonically evil, but not here aunt, is able to give them a lead on her Niece's whereabouts, and so with that information our 'heroes' track Maya down, with the fullest intentions of executing her on the spot, a technically justified action which is curtailed when Phoenix finds out that Maya is Mia's sister, at which point he changes tracks entirely, and decides that she deserves a fair trial, and so they decide to execute Morgan Fey in her place, simply because she tried to convince Phoenix to kill Maya, because she claimed that she was only motivated by the pursuit of justice, which given her canonical behaviour is treated as a deception even though as a survivor of that tragedy, she would have ample reason to want Maya dead, the fact that she's a survivor of the event is known to Nick Wright, but that doesn't even factor into his choice.

Maya is accused of destroying town with her powers as a total accident, and the accuser...dies, I think after being accused of lies, by Phoenix, simply because the two characters have a history of not getting along or something.