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...

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.