FANFIC REVAMPED, CORRECTED AND UPDATED. See details below.
My first fic evaaar! Woohoo! I feel so proud… sniff… Anyway, this fic follows six different plots happening at the same time:

1.- Daring Do, Rainbow Dash and Quibble Pants investigate "the greatest treasure of Empress Quetzalcoatl" in the mysterious Fortress of Teotihuacan.
2.- Rarity and Fluttershy get a Friendship Mission to Cloudsdale. Plot thread will no longer be followed.
3.- Applejack and Pinkie Pie, meanwhile, have to keep Ponyville's first Daring-Con running, while Twilight's Canterlot friends have adventures in it.
4.- Bon Bon, a.k.a. Special Agent Sweetie Drops, drags two unwilling ponies in her infiltration of a secret society that believes in the existance of creatures called "hyoomans". Story arc removed. Will be moved to its own independent fic.
5.- The Cutie Mark Crusaders investigate the mysterious disappeareances of nine ponies from Ponyville's history.
6.- Sunset Shimmer returns to Equestria.

Plotline 5 is the one including the crossover part of the story, and no, there will not be humans in Equestria. Have fun!

WARNING!: This fanfic contains spoilers for Seasons Seven, Eight and Nine, and all the Equestria Girls Specials! Proceed with caution.