Kyoji is a disciple of kendo and looks up to his teacher Tate Masanare. When he and Tate's fiancee, Yuka, watch Tate senselessly injure an opponent during a tournament, both of them search for answers. Tate starts acting strangely after the incident and believes that he is an Incan warrior. He asks Kyoji to spar with him and when he confuses his fantasy with reality, he almost kills his student.

Kyoji continues to try to find answers to why his teacher betrayed him, and why he is acting so differently. With Yuka, he travels to Peru in search for his teacher. When they arrive there, they get a history lesson about the Incan culture as it may pertain to Tate. Tate then reveals himself as a reincarnated Incan warrior, Yawaru, and tells Kyoji that he is his sworn enemy, Bilka.

Tate returns to Japan to recruit his old Incan associates. He makes them aware of their past lives using the power of the Earth, Iriyatesse. Meanwhile, Yuka and Kyoji are still in Peru looking for some insight on why the previous life has manifested itself into the present. They find out that Tate plans to tap the full potential of the Iriyatesse and use it for his own purpose. Reality is now irrelevant.

If only history could be taught from an anime point of view all the time, Nazca: Blades of Fate, is a story that includes historical Incan figures and parallels them to modern Japanese people. This is as close to a history lesson as you can get with anime. The main Incan figure involved in the story is Atahualpa, a warrior that proclaimed himself emperor right before the Spanish conquistadors came in and exploited their land. When Atahualpa made himself emperor, he had split the Incan forces into two factions because his half-brother, Huascar, was already the succeeded emperor. He recruited other tribes to fight his own people, thereby making him a traitor. This split gave the Spanish an easy advantage, and well . . .the rest is history.

The two main (Japanese) characters, Kyoji and Tate, are incarnates of two figures that lived during the time of the Incans. Tate was the loyal lieutenant, Yawaru, of the true emperor. Kyoji was a lieutenant on the side of the rogue emperor Atahualpa as Bilka. In reality (or Japanese life), the two are teacher and pupil; but in their Incan forms, they are bitter rivals. There is no sensible explanation to why Incan history possesses normal Japanese people all of a sudden because it seems like make-believe. But it is a purely different approach to anime. It is interesting to watch dissimilar cultures converge into a common plot of pride and love.

There is a scene between Tate and his student when he explains why he became a teacher. He basically states that the world is not in great shape, and it is not productive to be cynical and "turn your back on reality." He also emphasizes that people are a product of their imaginations. People can utilize their imagination to produce a better future for themselves. Thus, he became a teacher to motivate others to achieve that future. It is ironic that Tate himself turns apathetic on reality by depending on a previous existence. And instead of looking towards the bright future, he looks to the past and dwells on bitter issues. He has betrayed his own beliefs and therefore, also his student Kyoji.