The series begins as a guest visits a temple where Myo-Un and Ryu-Sang are living along with many other orphan children. This guest turns out to be an assassin who came to kill a certain someone who is the last child of a powerful family in Su country. The assassin's employer, who remains anonymous, wants to clean up every root of possible problems.

The assassin calls for reinforcements and attacks the lady of the temple, revealing that the lady of the temple is also another last descendent of another powerful family that was drawn out of Su country. Myo-Un, Ryu-Sang, and others are forced to flee the temple.

Thus, Myo-Un & Ryu-Sang's journey begins, and the assassin is still after them.

Note: Nabi: The Prototype is divided into six stories. Stories three to six features Myo-un and Ryu-Sang days in the temple before the story in Nabi began.