At the human colony of Ataraxia, Jomy prepares to leave his parents' house and take the adulthood exam. However, just as Jomy's memories are about to be wiped by the mother computer, Soldier Blue interferes.

At Educational Station E-1077, an academy for students who have passed the adulthood exam, Keith and Sam meet. When a transport ship collides with a military vessel in the docks and becomes isolated, Keith and Sam stage a rescue mission. However, with the station's mother computer preparing a purge of the affected region, they are running out of time.

Three years after settling on Nazca, Yui is killed in an accident. The old and the new generation are split more than ever about the future of Nazca and the quest to return to Terra, with the young Mu refusing to work on the ship. Meanwhile, Keith begins his journey to Silvester 7 to investigate the possible appearance of the Mu.

With the help of Grandmother, Keith quickly rises to become the leader of the human race and announces his plan to exterminate the Mu. A plan to ambush the Mu spaceship with a vast army before they reach Terra is immediately put in place.