It is during his first night on Mars that Ross has his nightmare, and it is much longer. When he is given his keys later by Eddie, his car is revealed to be a Ferrari, and to have robot-drive capability that Ross doesn’t use. Chris much admires the car, and his statements indicate that few people drive their own cars on Mars, as it is considered unsafe compared to robotic driving. Before finding Armitage, Ross visits Hu-Gite, the other major robotics company, but receives no help there. When D’Anclaude and Ross fight at the church, Armitage’s taking control of the crane is much more obvious. D’Anclaude’s reaction to her announcement that she is a Third is quite different- he is astonished, because her name isn’t on his list.
After defeating D’Anclaude, Armitage is badly beaten up, confused as
to her place in the world, and despairing of ever feeling at home. Her
solution is to throw herself into the water to drown. She nearly succeeds,
but Ross leaps in after he and pulls her to safety. Angry at still being
alive, Armitage leaps off into the night, leaving Ross confused. The final
scene shows various parts of St. Lowell and reveals how little the life
of most humans has been affected by what is happening, illustrated by the
uncaring treading of people on a fallen Kelly McCanon poster.
Meanwhile, Eddie has found a message from Pluto in Armitage’s mail and begins trying to decipher it. Ross then visits Conception to meet with Eugene H. Allen, Vice-president of Public Relations and a bit of a slimeball who stonewalls Ross’ inquiries. Ross sneaks back in and steals Allen’s access code, but still learns nothing.
While Ross is at the Jessica Manning crime scene, Eddie decodes the list of Thirds from Armitage’s mail. Lt. Randolph tells this to Ross, and also reveals that Lavinia Whateley was pregnant. This makes much more sense than the scene in Poly-Matrix where Ross is told by Eddie that Kelly McCanon was pregnant. After all, the first five dead Thirds were given to Conception to examine, and they would naturally want to hide the Third’s reproductive capabilities, so it seems unlikely a Third given to them would be allowed to be seen by TCS. Lavinia Whateley, on the other hand, was examined by Lowell first, and as Conception hadn’t got their hands on the body yet couldn’t hide the information. As Lavinia’s murder was cut from Poly-Matrix, however, it seems likely that other references to were ordered to be cut as well.
After meeting Julian, he reveals that he is incapable of maturing and
is trapped in his teenage body. After the battle in the memory server,
Ross passes out and the body of the second D’Anclaude is shown bobbing
in the water far below, seemingly dead--until his eyes open.
Ross tries to visit D’Anclaude in Shenora Hospital but they refuse to let him in. As he is leaving, he sees the doctor he just spoke to shaking hands with Eugene H. Allen from Conception. Later he is contacted by Chris, who tells him that the board from one of the puppet bombs looks identical to the board from a Third. Ross breaks into Allen’s house and physically threatens him until he reveals that Rene D’Anclaude, originator of the Assassinroids, is the man in Shenora Hospital, and that the other D’Anclaude was a robot. Ross leaps from the building just before one of Allen’s Seconds explodes, then receives a call on his damaged Navi from Armitage asking for help.
After burying Julian, Armitage decides to visit him in cyberspace. Ross
is able to go along as well due to his new nervous system but cannot enter
as fully as Armitage. As soon as he arrives he finds himself unable to
move, though Armitage appears floating gracefully on invisible currents
and frees him. They then find Julian’s backup and learn that all of the
murdered Thirds are in cyberspace as well. Ross again encounters a barrier
to his movement, and finds he cannot get close to Julian or the Thirds
while Armitage can. Julian confirms that the original D’Anclaude is in
Shenora Hospital, and they head there. Armitage attacks the second D’Anclaude,
but he doesn’t become pure data, as in Poly-Matrix; he simply explodes.
The OAV ends with the explosion of Shenora, leaving the fate of Ross and
Armitage in question.
After Ross and Armitage arrive at Dunwich Hill, they find Dr. Asakura, who mistakes Ross for spare parts he had ordered. Later, the attack on Dunwich Hill begins and so does the broadcast of that attack to the Seconds of Mars. The dead Thirds in cyberspace are revealed to be the source of the mysterious broadcast.
Several months later, Ross returns from Earth to Mars and is met by Armitage at the spaceport. He hands her a registered ID card for Earth giving her a new identity as Annalisa Bradford but she throws it away. Ross then suggests they go visit Julian, but she tells him she wants to wait until they are three. A surprised Ross learns Armitage is pregnant and is overjoyed, and the two of them drive into St. Lowell to make their new life together. This is quite a bit different from Poly-Matrix’s ending, where Ross and Armitage agree that they would like to have a baby together and start a new life.