It’s been two years since the fight between Godzilla and the MUTO Prime broke out near Ponyville in the Everfree forest. The Equestrians have calmed down since the incident and nearly forgotten about the threat of giant monsters invading their towns. It seemed everything was back to normal. Unfortunately, the evils of the past can always come back to haunt the present.

A massive meteor makes landfall in Appaloosa, creating a cause for alarm amongst the Main Six. It goes from bad to worse when the “meteor” turns out to be the prison of King Ghidorah, a enormous triple-headed extraterrestrial Titan whom is hell-bent on wreaking havoc on Equestria. When the destructive kaiju breaks free and begins his campaign of terror, Godzilla and the Main Six must once again band together to drive the villainous monster off their world.