I wrote a massive SGA crossover (Prodigal), but I played it straight and nobody found out about the aliens. :)
I will admit that my desire to write SGA is not at a high tide right now, but.. I don't think there is a Stargate Program in a world with SHIELD. The IOA and WSC are too similar in brief to make sense as separate UN-esque secret agencies funded by US blood and treasure. I think the stargate and its accouterments, when it is found, is handed off to SHIELD because they're the ones who deal with the weird shit and it just means that Nick Fury starts worrying about aliens before 2011. :)
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I will admit that my desire to write SGA is not at a high tide right now, but.. I don't think there is a Stargate Program in a world with SHIELD. The IOA and WSC are too similar in brief to make sense as separate UN-esque secret agencies funded by US blood and treasure. I think the stargate and its accouterments, when it is found, is handed off to SHIELD because they're the ones who deal with the weird shit and it just means that Nick Fury starts worrying about aliens before 2011. :)