- Watching Aoi get attacked by a mob and walk to her death to protect Mashiro. Even if She Got Better, it still hurts to watch.
- The end of episode 25, when Arika is reunited with her mother at last...and has to destroy her corpse and the system using it.
- Erstin's death. You know the writers are serious when they play a montage for you, replete with equally sad music. There's a reason episode 17 is the Wham Episode.
- And then, over the next few episodes, things got worse as all the cheerfully irresponsible behavior that used to be played for laughs stopped being funny.
- Also when Arika meets her mother for the first and last time in her life: (Arika twirling around girlishly) "Hey, mom! I'm a real Otome! It suits me, doesn't it?" And then the vision where Arika runs into her mother's loving embrace for just a fleeting instant. Both Mashiro and the viewer has a hard time keeping the promise not to cry.
- Erstin's last letter to Arika and Nina, in which she says she was told not to make any friends at the academy because of her mission as a Schwarz infiltrator, but she found herself becoming close to, and happy with Arika and Nina. She goes on to write that she still felt unable to go against her orders, but believed Arika and Nina were strong enough to do so. Nina, who by this point believes she has done too much wrong to go back, breaks down in tears; not only does this highlight the tragedy of Erstin's situation, but it also shows how broken Nina is.
- A private moment between Alyssa and Miyu, in which Miyu tries to reasssure Alyssa that Natsuki cares for her, but Alyssa remains unconvinced, and tearfully tells Miyu that she's all she has. Arika witnesses this scene, and is so disturbed by the possibility of crushing that hope that she's initially reluctant to fight against Miyu in the combat exhibition. Similarly, the part when it seems as though Miyu is about to die protecting Alyssa.
- The real Mashiro's death scene.