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.

Jomy reaches the Mu mother ship and learns of the true nature of the Mu. But the truth is too hard to handle for one who still believes himself to be human. Blaming the disruption of the adulthood exam on Soldier Blue, Jomy demands to be sent back.

Still unwilling to face the truth, Jomy returns to Ataraxia with the help of Leo. However, only a cold house devoid of signs of life awaits him. Soon both Jomy and Leo are captured and interrogated.

Having just awakened to his Mu powers, Jomy is going wild. As Soldier Blue goes out to help him, the Mu ship surfaces to draw away the human forces' attention. However, the battle does not look good.

Jomy has come to terms with his powers and undergoes training to control them. But time is running out as Ataraxia's forces discover the location of the Mu ship. In a desperate move, the Mu warps the ship from the planet's surface and starts their long journey towards Terra.

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.

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.

Eight years after Shiroe is killed by Keith, the Mu are still drifting through space in search of Terra. Karina brings up the topic of natural childbirth in conversation with Jomy and her friends, and Jomy decides that this is the future path for the Mu. When the ship comes across an abandoned human outpost named Silvester 7 in the Silvester system, Jomy proposes to stay there, renaming the planet to Nazca. Meanwhile, Swena is investigating the existence of Moby Dick, the rumored space whale, as well as the events that took place on Station E-1077 eight years ago.

The Mu have adapted to life on Nazca. The younger generation treat it as their home, but the elders are still bent on finding Terra. Karina gives birth to Tony, her and Yui's natural child. Meanwhile Sam, brainwashed by the computers, arrives on Nazca and attempts to assassinate Jomy who fortunately survives but causing Sam to lose his memories and revert to child-like bahavior. With all the recent events surrounding Nazca, Keith is sent out to investigate.

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.

Jomy is optimistic about the future of the Mu on Nazca, but Physis feels the "winds of misfortune" coming to the planet. Keith arrives and is shot down, captured, and interrogated by the Mu while his inexperienced crew abandons him and runs away. To Physis' surprise, Keith has the same vision of Terra that she does, although they couldn't find out more due to his strong mental block.

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.

Tony, along with Physis, is taken hostage by Keith. Karina goes berserk believing her son is dead and unleashes powers that damage sections of the ship. She is finally calmed by Jomy but in the end dies, due to her overexerting her powers. Keith uses the two hostages to slip by Soldier Blue and is taken home by Matsuka. Keith then contacts the military base and plans to return to eliminate the Mu.

Tony and other children on Nazca are suddenly in a state of hibernation now and the doctor is unable to bring them out of it. Keith assembles a crew and heads back to Nazca. A massive planetary scale weapon called the Meggido is introduced and the Members Elite plans to use this to eradicate the Mu's planet. The Meggido fires at Nazca and Soldier Blue teleports out of the ship to put up a powerful psion shield to stop it.

Soldier Blue's shield isn't enough to stop the Meggido. Immediately, Soldier Shin (Jomy) and the seven other hibernating children teleports to the scene and reinforces the shield. The majority of the beam from the Meggido is deflected but a portion still manages to damage the planet and kill the Mu taking shelter there. Soldier Blue uses his last ounce of strength and destroys the Meggido while Jomy gathers other Mu and warps out in the Shangri-la. In that act, Soldier Blue dies and Jomy takes his place as the leader of the Mu. Jomy orders the Mu to return to Artemisia to destroy the system that controls humans and to liberate all that reside in it.

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.

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.

On the way to Terra the Mu encounter a large human army near Jupiter. War and bloodshed ensues with lives lost on both sides. The human army is equipped with special spacecrafts immune to the Mu's psionic powers and as a result three of the blue-type Mu are killed. Tony who was struck with grief unleashes a large psionic wave that pulverizes a large section of the human army. Keith then decides to use the Mu captured on Artemisia as hostages and this angers Tony even further.

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.

Due to Jomy's persuassion, Keith requests a meeting between the higher ups of both sides. Jomy and the Mu warp close to Earth only to find a planet that is completely ruined and does not support life. What was awaiting the Mu was an ambush consisting of 6 Meggido units ready to fire. The firing of the Meggido weapons were stopped by Keith himself who decides to have talks with the Mu. The humans and Mu argue and bicker in a conference until Keith offers to take Jomy to Grandmother. They both go down towards the center of the planet where Grandmother awaits.

Swena broadcasts Keith's message to humanity about the truth behind Grandmother's ideals. The final truth about the Mu genes is revealed: before the creation of SD system, scientists discovered the mutant Mu genes and arguments ensued as to whethere they were only a flick of mutation or the next phase of evolution. Unable to decide, the SD system was programmed to leave Mu genes intact in birth control process, only to carry out the extermination when the gene carrier reached adulthood; the purpose was to check whether they could survive the stress and became the next phase of evolution. As such, the Mu survived, confirming their superiority; the only problem being that the Grandmother system has flawed programming and cannot accept the Mu. Keith broadcast this revelation for all humans to see, urging them to finally take over the decision and not relying on SD system any longer, while choosing to maintain the system for the sake of controlling human as a bet on human's future. Acknowledging Keith's decision, Grandmother's programming moved to phase 4: eliminate Mu factor in birth progress, and order Keith to kill Jomy. Keith & Jomy decide to fight Grandmother and are fatally wounded. Tony is chosen by Jomy to destroy the Meggidos pointed at Terra and to stand up as the next Soldier. Keith calls his subordinates to also destroy the Meggido units along with the Mu. The Meggido units are destroyed with the help of General Murdock who rams into it with his ship and Terra is saved from obliteration. Humans everywhere are shown rebelling against the SD system and Tony stands up as the next leader of the Mu to bring humans and Mu together. The final scene after the credits shows a reborn Earth as both the humans and Mu had hoped it would become.