The story takes place 50 years after the destruction of human civilizations by mad supercomputer Noah. The protagonist (default name "Hinata") is a young boy who is living peacefully with his foster sister Sasha and foster father Gib in desert islands. One day, a group of mysterious army attack their island. The protagonist and Sasha escape but Gib captures them.
Sasha tells the protagonist that Gib and him were "Hot Seeds", the project of sealing human survivors in hibernation chambers since 50 years ago, in order to preserve mankind and restore the human civilization after the "Great Destruction". Sasha reveals herself to be an android tasked to protect both Gib and the protagonist.
The motivation of the villains to catch Gib is to unseal the ultimate weapon "Black Mole" (クロモグラ), an "indestructible" mobile fortress that was created to fight against Noah, and Gib was one of the creators of it. Therefore, the protagonist have to save Gib to prevent the villains to lay hands on the "Black Mole".
