This story is a sequel to The Many Secret Origins of Scootaloo
When Scootaloo's attempt at flying causes her to crash into Twilight's lab, it sets off a chain reaction that causes Twilight to disappear, leaves the library in shambles and Scootaloo knocked out. A wave of purple energy rips through Equestria, leaving all to wonder 'great, what now?'
When Scootaloo awakens, she learns from the Bureau of Undoing Trouble from Twilight Sparkle that this world's Twilight is gone... and in her place are dozens of Twilights from different dimensions, tearing across the land. Worse, Nightfall Eclipse, a wicked Twilight from the antimatter universe, is assembling other bad Twilights to form The League of Evil Twilights, who seek to take over Equestria.
Now gifted with the ability to track down these Twilights, thanks to the explosion, Scootaloo will seek out these visitors from other universes in the hopes of sending them home and getting the real Twilight back.