Hm... Not paranoid enough. I've got it! Twilight Sparkle couldn't stand the thought of being wrong about something, so she personally researched and performed an unholy magic ritual to summon Nightmare Moon.
Speaking of Luna, what ever happened to her? All evidence indicates ponies are still just as diurnal as ever, but we've never heard a peep out of the ruler of night. Did she get executed for her crimes off-screen?
Seems to overlook the rather obvious continuity bug of Ponyville being razed to the ground at the end of "Swarm of the Century."