In a distant future where mankind has colonized the stars, life is being controlled by supercomputers. A race of psionics called Mu has emerged, and humanity fears and wants to destroy it. Staying hidden and attempting to rescue as many Mu children as possible before they are eliminated, the Mu have only one longing - to return home.

The plot of Toward the Terra spans a large number of years, jumping ahead multiple times, from Jomy's life on Ataraxia, to the various events on Station E-1077, to Jomy's founding of a Mu colony on a habitable planet, to the humans' invasion of said planet in order to eradicate the perceived threat, and finally to the Mu's return to Terra.