The Legend of Nayuta: Boundless Trails is set in two worlds: the main characters' home world, and a mysterious world called Lost Heaven. The main characters' hometown is Remnant Island, located in the center of Ciencia Sea, a vast ocean with countless islands. Shooting stars have been continually falling from the sky for some time, leaving much of these piled up on the island. Stones known as "Star Fragments" have been discovered in these areas. By shining a light on them in a certain way, people can see the phantom world of Lost Heaven.

The story follows Nayuta Herschel, a young aspiring researcher aiming to see what's further beyond the known world, who was just returning to Remnant Island for the summer, when he and his childhood friend Cygna Alhazen find themselves in the world of Lost Heaven through the guidance of the otherworldly fairy Noi, as they get involved in a plot to stop a madman and his right-hand man from destroying Lost Heaven and potentially Nayuta's own world in the process.