Set in Y-Academy, an elite school that only allows students with top class abilities to enter. The protagonist, Jinpei Jiba, and his unique friends take on the mysteries of the school as transforming heroes.
On a walk home, Keroro and Fuyuki stumble upon a hidden shrine. Upon exploring it, they end up causing damage to a shining orb within it. That night, Keroro finds a large X on his face, which causes him considerable distraught. The next morning, a breaking news story shows that the X has spread to more than just Keroro, giving the people of Tokyo telepathic abilities, including the Hinata Household and the Keroro Platoon. The Pekoponians seem to think this is a great gift, but the mark may actually be part of a Pekopon invasion older than time itself.