This section contains minor spoilers.
Killy is sleeping in class when Cibo wakes him up intime for Sanakan Sensei blast's his arm off. Pcell next to Davine Lu Linvega tells Dhomochevsky to do good in P.E. making him blush. Maeve tells on Baldanba-Kun for eating lunch during class. Mensab Sensei kills him, violently. Ivy places his hand on the hilt of his sword and Seu tells him not to give sensei any attitude, with his sword pointed at him. Maeve tells them to wait and they fight anyway. Some murder-soccer ensues leaving many dead. The principal say he doesn't like it when Sanakan shoots people but then affirms he doesn't have any problem with it. Killy is walking home injured when Cibo offers to walk home with him, a gust of wind blows up her skirt, he blushes and she promptly bashes his face in.
Part 2 "Tokyo and Nara Under One Umbrella"
The cast is on a school trip, a siliconlife woman tries to push Killy over a balcony overlooking the temple. Cibo asks Killy if he thinks this is weird for a school trip. Then there's some safegaurd "Deer" eating siliconlife people. Sanakan tells Ivy and Seu to stop fighting or else. Suddenly a giant jade Buddha statue with the two silicon life from chapter one Jenetalias and Meta-Jeannie. They express jealousy over not being in gakuen part 1, and not being featured as "Cool, stylish students." So they then fire a ray, Killy shoots down the statue ship and then it's revealed that the ray disassembles female's clothes in revenge Davine and Cibo seem more upset than Sanakan so Cibo knocks Killy's teeth out again.
Part 3 "Under the Tower of Blooming Sakura"
The two from chapter one Jenatalias and Meta-Jeannie reach the Structure Conversion Tower's console, and Meta-Jeannie accidentally runs the Moe Converter (Only for use in emergency situations) instead of the Structure Attribute Converter causing Meta-Jeannie to sprout dress ripping breasts that knock over the now vision impared Jenatalias. Everyone becomes Moe and nobody seems to notice or care. There's a shot of the girl's dressing room as they prepare for P.E. and Davine in a small bra. One girl has a cat tail and another has a pink katana. Iko has to use the bathroom so Dhomochevsky follows with much to Iko's protests. Iko get's upset and the scuffle causes them to break through the wall of the bathroom. They find out that the P.E. teacher Tsurujiru Sensei has found the remaining parts of The Female Clothing Disassembly Beam. In the following fight for the weapon they accidentally activate it, all students and teachers are effected. Killy gets a nose bleed while watching Cibo running a high jump and Cibo's drones laser holes into him upon landing. Iko is a girl with stripped panties. Sanakan shows up to kill them and the P.E. Teacher but they dodge and she destroys the The Female Clothing Disassembly Beam (the handheld beam remains). Student Council President Seu shows up to stop Jenatalias and Meta-Jeannie, they're quickly defeated and everyone goes home unhappy, but still moe.
Tsutomu Nihei himself drew lewd (mostly topless) images of Sanakan, Cibo and Iko.