Toward the Terra

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.