Sigma and Phi have both reached 9 points, but they both decide to search for Quark before opening the number 9 door and leaving. After looking around the facility, they find Quark in the treatment pod in the Treatment Center, and they carry his unconscious body to the number 9 door, which Phi opens. Sigma is unsure if something ought to be done about Luna, but Phi insists they should leave immediately with Quark.
Sigma and Phi leave the facility, but as soon as Sigma is standing on the exit elevator, he hands Quark over to Phi and runs back into the facility! Phi is shocked and baffled as Sigma traps himself, while Sigma comments that he finally feels free. Sigma goes to the Botanical Garden, knowing that Luna will be waiting there.
Sigma talks to Luna about the murders that have occured in the facility, and explains that he believes Luna didn't commit any of them. Luna asks him how he knows, and he refers to information that came from an alternate history - when Luna questions him about this, he dismisses her objection. Luna points out that he doesn't know for certain that Luna couldn't have committed the murders, and Sigma replies that he does - Luna is bound by the Three Laws of Robotics, and could not possibly have harmed a human.
Luna is amazed by Sigma's trust and by the sacrifice he has made for her, and explains what has happened. She states that she put Quark in the Treatment Center after Zero-Jr opened the door for her, and she also removed his bracelet by wrapping it in aluminium foil from the Crew Quarters, thus damping any electromagnetic signals to it and making the bracelet believe Quark's heart had stopped ("it was that easy all along?" replies Sigma). Clover blamed her for Alice's death (although Alice actually killed herself) and injected Luna with tubocurarine in the Crew Quarters. Since Luna was required to behave as a human, she collapsed when this happened, although this wasn't actually her choice - Zero Jr knew she was supposed to do that too, and switched her body off.
She also tells Sigma that she was given instructions by the old woman before the beginning of the game, that she should monitor the players, make sure things run well, and try to help them. Sigma asks if this means that the old woman is Zero Sr, but Luna replies that she is not, but she was working with Zero Sr on a "project" - but Luna doesn't know what the project is. Dio broke into the facility through the number 9 door (which wasn't locked before the game began) with the intent disrupting the project by joining the game, which he aimed to do by killing the first person to leave their AB room - but Zero Sr and the old woman predicted this and intended it. Zero Jr was instructed to let Dio into the base, and the old woman explicitly told Luna to move her body into Luna's AB room if she was killed.
Luna admits that she does not have long to live at this point, and Sigma asks why. Luna explains that she was not actually supposed to be re-activated to have this conversation - her "brain" process, which is in Zero Jr's mainframe, attacked the mainframe to re-enable her body. She has also broken the First Law by allowing several humans to be harmed in situations where she could have prevented it. And the tubocurarine injection, although it would not kill her, has caused the ABT surrounding her endoskeleton to begin to atrophy. Gradually fading out, Luna hugs Sigma, saying that she wishes she could be with him like this forever, and then adds, ".. doctor."
On the PS Vita version, getting this ending gives the achievement Tears In The Rain, a reference to the movie Blade Runner.