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.

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.

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.