The Dogma Kingdom attacks the Matagi (mountain tribe) village of Yamabiko to steal the sacred Flying Dragon Fortress and wreak havoc all over Japan. Six children from the fallen village take refuge in a nearby town, keeping their identities as Matagi citizens a secret. Kamen Rider Super-1 must protect these children from the Dogma Kingdom, as they hold the secret to the Flying Dragon Fortress' weakness.

Two men, tired from work, visit the town of Chichibu to enjoy their favorite hobby - exploring caves. But little do they know, the town has been secretly protected by the descendants of the righteous Shinobi ninja since the Sengoku period. The two unlucky friends accidentally break a spell that awakens two colossal beasts, Jaron and Goura. The area’s rival clans manipulate them into a fierce battle, bringing chaos to the area. But a righteous female ninja steps up, wanting to stop the destruction and restore the seal. Can she defeat the evil ninjas that stand in her way before Chichibu is completely destroyed by two kaiju?