Note: This story takes place between the 7th and 8th seasons of FIM, taking the place of the 2017 movie. For my Marvel/DC Teen Titans, this takes place after the "In Times of Crisis" story which retconned their original origin story I had written.
While setting the Festival of Friendship, Twilight Sparkle and her friends are attacked by Amora the Enchantress and Skurge, the two of them are quickly followed by the Teen Titans comprised of Marvel and DC heroes. After the two villains escape, the two groups decide to work together as Robin (Tim Drake) offers his help along with Scarlet Witch, Spider-Man, Ms. Marvel, Supergirl, and Batgirl, even when the Titans themselves are having issues based on recent events.
But as the two groups work together, they will discover that something much darker is about to occur as Twilight will have to face her fears and concerns. If the two groups can't stop the coming threat, Equestria as well as other universes are doomed.
Thumbnail art by https://www.deviantart.com/small-brooke1998