The human population of Earth is suddenly struck with amnesia. Humans forget all knowledge of technology and civilization falls to ruins. The Japanese hero, Wataru, regains knowledge of civilization with the aid of a white boy Johnny. On his travels, he meets a young (very white) woman Sophia, who seems to be the only person with memory.
Wataru: young Japanese male, initially amnesiac, re-educated by Johnny
Johnny: wheelchair-bound silver blond boy who is part of a military experiment. His increased mental capacity preserved him from the damage of the "amnesia" epidemic.
Sophia: Silver haired woman, member of an alien race that has been watching over earth since the beginning of humanity.
When Wataru first meets Johnny, Johnny is squaring off with a black man wearing only briefs. The black man has the power of levitation and is able to cause earthquakes. According to Wataru's own words, he "instinctively" felt he should help Johnny. He steps into the fray, but just as the black man turns on Wataru, Johnny kills the black man with a pistol shot.
Johnny tells Wataru that both Johnny and the black man were part of a military experiment. The black man was given the power to cause earthquakes, but when the amnesia set in, the doctors and nurses neglected to care for him, leaving him tied to his bed till he went insane and broke loose.
Later, Wataru and Sophia run into a young red-headed woman who is the intended sacrifice for a mechanical god. Humans, having lost their memory of technology, now pay homage to a giant construction crane that they think has a life of its own. Wataru saves her from being taken for sacrifice -- incidentally, all the sacrificial victims required are attractive young women -- but she eventually returns to face the monster.
It turns out that a black man who passes himself off as some kind of high priest is operating the crane. He demands young maidens for sacrifice from the people. The black man (the viewer never gets to see his entire face, only his big Afro and his maniacal grin) turns the machine on the people. The young redhead is killed and Wataru, in righteous rage, destroys the crane (and presumably the black man) with one pistol shot.
There are no other actual human villains in A Wind Named Amnesia. It seems too much of a coincidence that both villains are black while the beautiful and kind people Wataru encounters are all white.