The only fanfic that I write takes place in the Stargate universe, around the time between the final 'death' of Anubis and the advent of the Ori.
My only "Mary Sue" characterization is that of an archeo-technologist working a dig where a lot of Ancient artifacts are being found. He's not much of a hero, nor does he "get the girl" like the heroes do. He is an Aspie, however ... 
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The mere fact that science may not yet adequately explain an object, event, or experience does not mean the immediate explanation should automatically default to a conspiratorial, extraterrestrial, paranormal, or supernatural cause.