Crono's party heads to Geno Dome in 2300 A.D. where they find out that the Mother Brain has taken over the robots and intends on eliminating the remaining organic beings allowing the machines to rebuild the planet in her vision.
While fighting their way through Geno Dome, they run into Atropos XR, a female version of Robo's droid model. She explains that the humans reprogrammed him from his original programming...kill humans. Robo refuses to believe it and wants to fight her. After Robo wins the battle, Atropos' memory slowly comes back. She then realizes that Mother Brain overrode her programming to make her kill humans.
The party then proceeds through the Dome and eventually defeats Mother Brain.