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.

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.

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.