Examine the body and after the scene, examine the body again. Examine the key nearby. Makoto doesn't recognize it, so its origin is a mystery for now. Head down to the data center on the fourth floor and examine the door. After the scene, examine the door to the data center again to enter. Examine the door marked by an image of Monokuma at the back of the room, as well as the many screens around it, the TV to the right, and finally, the monitor showing a map of the world in the center of the room. After some scenes, Makoto finally receives Monokuma File #5, commencing the investigation.
Garden
Examine the Knife at the Crime Scene. This is the same knife that disappeared from Makoto's desk, as well as the one held by the masked figure in his room. Could Makoto have had some involvement in the crime without even realizing it? Examine the familiar-looking Fragments Near the Dead Body before finally examining the body itself. Examine the hand, adorned by Fake Nails that look long enough to get in the way of everyday activities. There's also a distinctive Tattoo on the Right Hand of some canine creature; could this be a hint regarding the body's identity? For now, it remains unclear. Lastly, examine the chest area for the Exploded Body Analysis. The bottom half of the body is dry, while the top half is wet. Makoto threw water onto the top half of the body in order to put out the fire, but is that really all there is to it?
Examine the Chicken Coop Chickens. They seem to be fine, except for the fact that one of the five chickens is missing. Yasuhiro claims that during his last visit before nighttime yesterday, all five chickens were accounted for. Something must have happened between last night and this morning, but does it have anything to do with the murder? Examine the control panel nearby for the Sprinklers Bullet. Monokuma mentioned the sprinklers would go off every morning with no exception, though the body wasn't wet, which would indicate that the murder took place in a very narrow window after Yasuhiro and Byakuya visited but before 7:30 in the morning. Enter the tool shed. Everything is just as it was before, except for the Tarp on the floor. Examine it for a closer look; one side is wet and muddy, while the other is dry. It seems as if the clues gathered from the control panel and the sprinkler are related in some way, though Makoto can't be entirely sure until the trial.
Speak to Byakuya and react when he says he wants to [talk]. He describes the events of last night and the day before in great detail, singling out Makoto as the one person without an alibi. Nevertheless, this earns you Byakuya's Account. Afterward, make sure to speak to Yasuhiro and Aoi. Aoi makes Makoto recount the Body Before the Explosion. The body was masked and wearing a white coat, and just as was described in Monokuma File #5, a knife could be seen through its chest. Fittingly, there was blood pooled on the body's chest, but strangely, there was no blood to be seen around it. What could that indicate? On the other hand, Yasuhiro wonders When the Body Was Found. The timeline seems messy due to the various factors involved, though Makoto can be sure of the timing of some events: he woke up at 7:00 AM and met with Aoi thirty minutes later at 7:30. Following his meeting up with the others and journeying to the headmaster's office, Toko discovered the body sometime around 9:00 AM. But when was it that Monokuma announced the death?
Makoto still has a few other places to check, so speak to Byakuya before leaving for access to Kyoko's room. Start by heading to the gym.
Gym
Examine the dismantled Monokuma on the floor. Makoto's suspicions are confirmed: the bomb that the group found inside Monokuma is missing, which must mean that the Fragments Near the Dead Body are actually part of a bomb. This would certainly explain the explosion that occurred when the group discovered the body, but who would have stolen it and set it at the crime scene?
With nothing else to see here, return to the garden and speak to Byakuya.
Kyoko's Room
Speak to Byakuya by Kyoko's room, then examine the door to enter. Examine the Woodblock Key on the table. Byakuya seems to think it belongs to one of the lockers in the dojo, giving you another lead. Speak to Byakuya, then examine Kyoko's bed. Under the sheets is Mukuro's Profile, describing supposed sixteenth student Mukuro Ikusaba, otherwise known as the Ultimate Soldier. As is made apparent by her title, Mukuro had a great interest in the military, even going so far as to join an overseas group of mercenaries known as Fenrir. Even stranger than this profile is that you are provided with Monokuma's Account shortly afterward. Monokuma confirms that there were sixteen students, not fifteen, at the start of the killing game. He also mentions that Kyoko wears gloves in order to hide hideous scars on her hands, of which there were none of on the corpse.
With this new information and the woodblock key, head to the dojo.
Dojo and Archive
Examine the last locker to the right to find Titanium Arrows. The arrows are thin in size, but also incredibly strong due to their sturdy material. There's also a wad of Bloody Duct Tape within the locker. The bloodstains seem to indicate some relevance to the case, though it isn't clear how. Byakuya then directs Makoto to the archive for information on Fenrir. Once in the archive, speak to Byakuya to learn more. As it turns out, Fenrir is an elite fighting unit based in the Middle East, and its members get the group's logo tattooed on them once they join. Could this mean that the corpse is actually Mukuro's?
With the investigation now concluded, head to the courtroom as usual, though you haven't collected all Truth Bullets just yet.
Courtroom
Speak to Kyoko for one final Truth Bullet, Kyoko's Account. She says she's been absent for so long because she was busy exploring the second floor using "Monokuma's secret tool," which supposedly allows her to open any lock in the school. The area she was exploring lacked surveillance cameras and monitors, which was why she missed the dead body announcement completely and was late to the investigation.
With that mystery out of the way for now, examine the elevator to proceed to the class trial.