Hana no Kioku consists of five episodes, all of which can be accessed from the main menu, in no particular order:
1. The young school girl Chiko is taking a subway train and is sexually molested by what she thinks is a chihan (a person with the popular Japanese "hobby" of touching young girls on the trains). However, the chihan turns out to be a young girl named Kiko, who wears a rather elaborate disguise.
2. An episode dedicated to another popular Japanese theme: tentacle sex. A young girl named Mei thinks about anime stories and brave heroes who defeat monsters; at that moment, she is sexually assaulted by a horribly-looking giant squid monster.
3. Mei is back in school, but this time she is not the player-controlled character; the latter is now a female teacher named Sumi, who has ordered Mei to stay in the classroom after the lesson, in order to have sex with her.
4. A school girl named Saki is sick and is lying on the bed in the school hospital. From that point, the story can branch two different ways: either she is being raped by Sumi, or seduced by the nurse Aki.
5. Back to Kiko from the first story; she is the playable character now, and, depending on the story branch, she either waits for her boyfriend and has sex with him, or goes outside in a disguise already seen in the first episode mentioned.