One of the Immortal Nine, Phantom Verde, is said to be staying in a certain Nean settlement, but only authorized personnel are allowed in. While walking around town, Rouge meets a doctor who works in the settlement and seeks his help to get inside.

Rouge is held by the CFN under suspicion of murdering Juval. Naomi advises her on how to escape, but Rouge suspects that Phantom Verde is involved and chooses to stay. Meanwhile, the police dispatch a security force to the Nean settlement...

The imprisoned Rouge is lost in an illusion that can't be called either a dream or a memory: her life just after she was born, her days with her kind older brother Gene and her father Roy... as well as an unfamiliar woman and a masked man.

A murder occurs on the ship carrying Rouge and Naomi. The killer is captured by a surveillance camera, but another camera shows the same person elsewhere at the same time. Then another murder occurs, and the killer on camera looks like Naomi...

Naomi meets with Gene Junghardt as more pieces of the puzzle are revealed. Meanwhile, Rouge, who is due to be transferred to Ochrona, has an unexpected reunion.

Rouge reunites with Gene and they visit Dr. Junghardt's Memory Library. Rouge traces his memories to learn about herself, Code Eve, and Dr. Jung's goals. Then a girl shows up claiming to be Rouge's younger sister, Cyan...

As Rouge struggles against Aerkos, Silvia, and Grauphon, Eden shows up to save her, but it turns out he's also part of the Immortal Nine. A Usurper ship and Cyan show up, and the situation spirals into chaos. Could Cyan really be Rouge's sister?

En route to Venus, Rouge and Naomi learn that Cyan has stowed away on their ship. She's convinced Rouge is her big sister and insists on traveling with her, despite Naomi's protests. Ahead of them, Gene reaches Venus and meets the Puppetmaster...

After making an emergency landing on Venus, Rouge's group enters the Cloud Plant to find Gene, but Silvia picks up on their movements. As Gene looks on, the Puppetmaster begins to talk about his mother, Eva Kristella, and her creation, Code Eve.

Rouge and Naomi find Gene, but his behavior seems off. Eden battles Grauphon, both fighting for their convictions and the people they love. And Cyan is captured by the Puppetmaster, robbed of her consciousness, and forced to play a certain role.

The true identity of the Puppetmaster is revealed. Rouge, Silvia, and all the others listen in shock as he explains his plans and the world he wishes for. Were Rouge and the rest no more than puppets in his play?