In the RPG Mode, Granblue Fantasy: Versus features a standalone storyline where players embark on a journey visiting the featured locales within the fighting game. The player takes control of Gran and company to fight other notable characters within the Granblue Fantasy universe visiting various islands and uncovering the mysterious force surrounding the violence and chaos that ensues through quests. Along with meeting the main cast of characters, the player is also introduced to their backstories and existing relationships with other characters.

In a world where adventurers roam the skies on airships, and the floating islands of the Skydoms lead their way, the Grandcypher—an airship of massive proportions—sets out on a magnificent journey, traveling the islands, and picking up a veritable army of sellswords, knights, and mages along the way… However, these heroes of the sky will soon embark on a brand-new adventure, where battle and glory await!