Set some years after the original plot, this film follows Naomi Armitage as she investigates a military attack on robotics plant on Earth.
It had been several years since the events of the previous OVA. Naomi Armitage and Ross Sylibus, now living under assumed identities, are living in St. Lowell on Mars, along with their daughter Yoko (which Naomi had given birth to), as husband and wife. Ross now works for a company seeking to restore oceans to Mars by using ice asteroids. However, a new effort to restore the Third project prompts Naomi to travel to Earth to figure out what is happening. Meanwhile, Ross saves a facility from a group of terrorists and is declared a Martian hero.
When Armitage arrives on Earth, she confronts Colonel Strings over the slaughter of new thirds. But then he is shot by agents of a Earth Robotronics Corporation. Its vice president, Demetrio Mardini asks Armitage to give the data on how thirds can conceive so humanity can create a race of beings who exist to serve. She refuses so he resorts to force and unleashes a robot that scrambles her eyes. She manages to use her telepresence abilities to hack into its system and overload it. She then escapes but is damaged and is found by a repairer third named Mouse, who prides himself on his skill and frequently brags that he\\\'s a genius. However, Mouse is also an informant to Demetrio and presents what data he found on Armitage; but he only got the recent data and Demetrio wants the conception data. Mouse claims that he didn\\\'t know about the conception data, and also that if it existed it would be with what he gave him; but Demetrio refuses to believe either of these and tries to brutally force it with two clones of Armitage, who severely injure Mouse. He doesn\\\'t get anything and throws Mouse in the trash. Mouse swears revenge.
Back on Mars, the prime minister sends Ross to Earth to represent the planet in the support of robot rights. However, Demetrio\\\'s agents captured Yoko while Ross was away from the hotel. If he doesn\\\'t go against the rights bill, he won\\\'t see Yoko again. With a little reluctance, Ross remains neutral on the bill. But Demetrio\\\'s agents don\\\'t fill their deal and try to kill Ross but he is saved at the last minute by Armitage. Together, they vow to rescue their daughter.
They infiltrate Demetrio\\\'s compound; Armitage deals with Demetrio while Ross saves Yoko. The same robot Armitage encountered earlier had been upgraded to withstand her telepresence attack. Meanwhile, Ross manages to locate Yoko in a freezer. Elsewhere, Demetrio demands the secret. Armitage lures him closer, presumably to tell him what he wants to know; but she ends up kicking him in the crotch and telling him that third conception isn\\\'t simply data, it is about true love. With that she escapes again, forcing Demetrio to unleash the clones on her. She manages to evade the two and meets up with Ross and Yoko. Yoko is overjoyed to see her mother but recoils when she sees Armitage\\\'s metal shoulder that was scraped off by the clones. Just then, they attack. While Armitage holds them off, Ross and Yoko make their way to an unused space elevator. It is here that Yoko shows that she has a photographic memory, leading them to the space elevator whose location she determined from a map she saw minutes beforehand (Ross comments that she is quite the little genius). Soon, Armitage flees to Mouse, who repairs the damage and gives her a program that will allow her to go beyond her limited fighting abilities. He tells her that the password is Heaven\\\'s Door; but that if she exceeds more than her internal battery can handle, she\\\'ll be knocking at the Pearly Gates for real. She also has him do her one more favour broadcast the footage of Robotronics attempts all over Earth and Mars (upon seeing it himself, Mouse comments, Even I think it\\\'s inhumane, and I\\\'m a robot!). This compels Demetrio to command the clones to prevent the family from leaving. After an intense fight both are beaten. Demetrio tries firing on the shuttle they\\\'re on only to be killed by the last remaining clone, who is at the time controlled by what was left of Julian Moore in Armitage III Poly-Matrix. Without Demetrio\\\'s authorization, the turrets do nothing. A hologram of Julian Moore then appears, wishing the family goodbye; this is presumably meant to be confirmation that while Julian\\\'s body was destroyed, he is still, in a sense, alive. The movie ends with the family enjoying a day at the beach on Mars, on Naomi\\\'s birthday.