Four years after Sam enters E-1077, Shiroe, a top student with a rebellious attitude, arrives at the station. Shiroe, who is the same child whom Jomy tried to save previously, tries his best to challenge Keith. His verbal provocations eventually lead to Keith hitting him. Meanwhile Swena, tired of trying to win cold Keith's heart, decides to marry and leaves the station.

Keith is troubled by his own nature and Shiroe's words, and questions Sam's statement that he is different from others after all. Shiroe, while investigating Keith's origins, uncovers the secret of Mother Ilaiza's genetic breeding program. Jomy, as the leader of the Mu telepathically broadcasts a diplomatic message causing everyone except Keith revert to child-like behavior.

Keith finds and shelters Shiroe, who is fleeing from a psychic exam. Shiroe is arrested while in Keith's care, but manages to stir doubts in Keith. The next day, much to Keith's surprise, everyone's memories of Shiroe and Jomy are erased. However, as Jomy attempts to communicate yet again, Shiroe flees the station and is shot down by Keith.

Jomy continues to interrogate Keith but ultimately fails. Tony attempts to take Keith's life using his power but Keith manages to throw a broken shard at Tony and immobilizes him. Meanwhile Soldier Blue awakens from his long sleep while Matsuka flies to rescue Keith from capture. Episode ends with Keith meeting with Physis.

The seven blue-type children, including Tony, are now fully grown and are used as deadly weapons against the humans that get in the Mu's way. Due to their power and ruthless antics, the new blue-types are feared and a generation clash emerges. Jomy recognizes this but chooses to ignore it to reach the goal ahead, Artemisia. Keith, Swena and Sam are reunited and Swena hands over Shiroe's Peter Pan book. Inside the book Keith discovers a chip with a visual recording of his own birthplace. Keith decides to return to Educational Station E-1077 while Jomy and the Mu obliterate the humans' defenses and reach Artemisia.

Keith and Physis discover the shocking truth that they both were artificially created through a process of genetic manipulation and a product of many failed experiments. It becomes evident that Physis is not a Mu, but an artificially created human given powers by Soldier Blue in the past. Jomy returns to the amusement park where he was supposed to have undergo his adulthood exam by Terras #5 and completely destroys Terras #5 this time. Keith puts Mother Iliza and Educational Station E-1077 on a self-destruct sequence and a new computer system called Grandmother is reinstated. With Terras #5's computer system destroyed and the path to Terra cleared, Jomy decides to venture there along with the other Mu.

Tony decides to take matters into his own hands and tries to assassinate Keith. He uses telekinesis to suffocate Keith but it ends prematurely when Matsuka jumps into the scene. Tony tries to deal the finishing blow but instead kills Matsuka who jumps to shield an unconscious Keith. At that moment, reinforcements arrive and Tony was forced to retreat.