Before the chapter even begins, enter the dressing room to speak with Kyoko. After the scene, enter the boys bathroom. The storage closet can be found behind the door past the stalls, at the very back of the room; examine it to enter. Once inside, examine the back wall to find the entrance to the secret room. Examine the massive book shelf. After the scene, examine the book shelf again. After another scene, enter the gym.
The next morning begins, as usual, in the dining hall. From here, head to the newly-opened fourth floor. Attempt to open the doors to the data center and the headmaster's room. Both rooms are inaccessible for now, which is as good an indication as any that the mastermind is hiding valuable information within. Nevertheless, enter the office and examine the photo on the floor for another puzzling hint. Afterward, enter the chem lab and examine the cabinets filled with all sorts of chemicals, then enter the music room, where you can speak to Kyoko. When given the option, choose not to tell her. She'll be disappointed in Makoto but this is the only way to progress the story. Back in the dining hall, speak to Aoi, Yasuhiro, Sakura, and Kyoko to trade information.
In the dressing room, speak to Genocide Jill after the short conversation with Toko and examine the laptop. The next day, head to the dining hall and speak to Sakura. After two segments of free time, head to the gym, and then the dining hall again. After two more segments of free time, return to the dining hall for a troubling scene. Speak to Aoi and react when she mentions a [fight]. Speak to Kyoko and react to [that issue], then speak to her again and react to [something else].
Back in the dressing room, examine the laptop. When given the option, select the secret room. Begin heading there by going to the boys bathroom on the second floor, just as before. Once inside, examine the storage closet and then the back wall to gain access to the otherwise empty room. Examine the desk to find a network cable for Alter Ego. The next day, answer the door in Makoto's room by examining it, then speak to Aoi out in the hallway for some bad news.