It has been thirteen years since the mane six disappeared, leaving their children and husbands behind, and upon finding out, Tirek, Chrysalis, and Sombra join forces and start to march towards Ponyville to take over Equestria, but when a messenger warns Twilight's husband, Flash Sentry, he sends his son and the other six's children to find the elements.

P.S. this is an anime-ish story so things you wouldn't usually see in the show will happen...fighting, blood and gore, random thoughts, so on and so forth, main reason for alternate universe tag.