Start by examining the body for the Status of Sakura's Body. The details of the Monokuma File check out; there's some blood by her lips that would indicate vomiting blood, but no other apparent injuries. Why did she end up vomiting blood then? Examine the Polka Dot Candy Wrapper by her feet. Aoi mentions that she recognizes the wrapper, as it belonged to a candy she had given Sakura. Examine the red Glass Shards on the Floor behind her, which appear to be parts of a bottle. Makoto also spots a Figure on the Floor, depicting Monokuma holding a chess piece. Why would that be there? Examine the bottles lined up on a cabinet to the right to find the source of the glass shards and Monokuma figure. A Monokuma Bottle seems to be involved in some way with the murder.
Examine the Magazine Shelf Bloodstain, which is quite a distance away from the body. This must be the victim's blood, but why would it be all the way over here? Examine the door, which was mysteriously blocked off to create the locked-room murder. Examine the chair, which was used to block off the door. The door and chair indicate that the Rec Room Door was mysteriously blocked off from the inside, but by who? Finally, examine the plastic container by the door, which turns out to be an Empty Protein Drink. This wouldn't be too strange under the circumstances, as protein drinks were a favorite of Sakura's, but Kyoko points out that it somehow ended up above the shards of glass that once formed the window to the door, smashed by Makoto only a little while earlier. For the final Truth Bullet, the Locker Handprint, examine the locker in a corner to the right of the room. The powdered handprints look fresh, so it seems someone must have been hiding out within the locker, but they couldn't have produced the locked-room murder by stealthily joining in with the group that discovered Sakura, since all bodies were accounted for. What could be the cause of them then?
Speak to Aoi for Aoi's Account. Apparently, Sakura had invited Byakuya, Toko, and Yasuhiro to meet her in the rec room around noon which, according to the Monokuma File, is precisely when the murder occurred. Aoi reasons that with this information, one of those three must be the murderer. Speak to Byakuya to confirm these details and obtain Byakuya's Account. He claims he had no involvement in the murder as he didn't even bother meeting with Sakura due to feeling threatened. Exit the room and head to the dorms.
Makoto must now verify Aoi's Account with the other two suspects mentioned by her. Begin by examining Toko's door to speak to her. React when she says [talk] to press her about Sakura. She confirms that she received the note, but denies ever having seen her, earning you Toko's Account. This leaves only Yasuhiro as a suspect if Byakuya and Toko are to be taken on their word. Examine Yasuhiro's door around the corner to speak to him. React when he asks if you [need something] to press him about Sakura. Yasuhiro mentions both Toko and Byakuya having received invitations as well, even though he should have received a note addressed only to him. Again, Yasuhiro denies having met with Sakura, but as he attempts to escape, he drops some Pocket Trash that looks eerily familiar. Exit to the chem lab.
Examine the large shelf of chemicals. There's some strange powder laid out in front of it. Start by examining all shelving units of the Chem Lab Shelf: A, B, and C. A contains dietary supplements and medicine, B contains reagents meant to bring about chemical reactions, and C contains dangerous chemicals and poisons. However, there's something odd about unit A: a poison from unit C has somehow ended up there. Could it have been placed there accidentally, or with malicious intent? On the floor, examine the bottle to determine the Source of the Powder, a bottle labeled C-4. Examine the Footprints in the Powder. Makoto and Byakuya determine via sketch that someone made the footprints on their way to the left side of the shelf, right where unit A is located, and nowhere else. This also occurred around the time of the incident according to Byakuya's account, indicating a connection to the murder. Return to the rec room to finalize the investigation with a bit more evidence.
Examine the bottles on the cabinet again to perform the Monokuma Bottle Experiment. When Makoto gathers up the shards of glass on the floor that seemingly make up a Monokuma bottle, they come out to be heavier than the other Monokuma bottles. What could be causing the shards from the floor to be heavier than the bottles that are still intact? Next, examine the magazine shelf. An upside-down magazine holds an unexpected surprise: the name "Toko" is written inside, and it appears to have been done with Sakura's blood. This earns you the Bullet Magazine Dying Message, but could it really be that easy? Examine the body one last time. Some Yellow Powder can be found on her shoe. Makoto also receives Kyoko's Examination Summary: both of Sakura's hands are completely free of blood, and she apparently suffered two blows to the head, not just one. Whether or not this information is important will become clear in the trial.