Our story begins when seventeen vessels mysteriously blow-up and sink on the nearby Odo Island. Professor Windy Whistles, her daughter, Rainbow Dash, and Fluttershy head to the island to investigate. Soon they witness a giant monster the locals call Gojira destroy the area.

Meanwhile Rainbow Dash meets her marefriend, a secluded scientist named Twilight Sparkle. She makes Rainbow promise to keep her secret about her research. When Rainbow agrees, Twilight reveals a lethal weapon she developed called the Oxygen Destroyer. Soon, Gojira’s presence threatens Ponyo and other Japonies cities. The army and navy find they aren’t capable to stop it either. Rainbow Dash breaks her secret, and discloses Twilight’s weapon to her lover, Fluttershy. Now, they try to convince Twilight to use the weapon to stop Gojira.