My theory is that
Mukuro Ikusaba was a Monokuma spy, infiltrating the students under the guise of either Celeste Ludenburg or Junko Enoshima - most likely Celeste.
So, after that shocker of a trial, I did some thinking about the oddities in the case. Let's establish a few things right off the bat.
Firstly, we know that the
Fifth Trial was rigged
. Monokuma declares Kyoko the blackened in the alternate end, and Makoto the blackened in the normal route. Also, he has no problem declaring Makoto, who we know is innocent, to be the blackened. That means that Monokuma doesn't care who he fake-executes as the blackened, as long as someone takes the fall. This would explain the generic execution method rather than the very specific and ironic ones he used before.
We also know that if a student was the killer, Monomuma would have no problem letting the trial go ahead. It's what he wants, after all, why he brought them there in the first place. Monokuma's weird attempt to rig the trial means that he either does not want the students to unearth the real murderer, or there is no murderer tk be found but he wants a scapegoat. The former seems... I can't think of a reason why he'd do that. I can think of a reason why he'd do the latter - because he is the murderer. This makes perfect sense. Monokuma, seeing that nobody there was going to murder and continue the game, decides to spark things along by killing Ikusaba and pinning it on one of them to fracture them. Another piece of evidence supporting this is that the other four had airtight alibis, which leaves Kyoko and Makoto as the only ones without an alibi, as was brought up in the trial. We know Makoto is innocent, and in the unlikely event Kyoko is the killer we know Monokuma has no problem punishing her(see the alt end) so it makes no sense that he'd let the frame on Makoto go ahead and pretend it was true. Finally, on a pragmatic note, I do not think Kyoko could win a fight against the Ultimate Soldier.
So Monokuma was the killer, and he's framing Kyoko/Makoto for it. We know why he did it - to keep the game moving. So what are we missing here?
1) Why was Mukuro Ikusaba not with the original 15 students?
2) How did Monokuma overpower the Ultimate Soldier(I could see him using remote controlled guns or whatever to kill her, but remember she got brained by a bundle of arrows)?
3) Why was Ikusaba's face covered by a mask?
Let's start with 3). The obvious answer is that Monokuma does not want them to know about Ikusaba's existence. Here's the problem - it's not a secret that could be viably kept. Even if he predicted Kyoko walking off, he couldn't have predicted Kyoko not passing on the information about Ikusaba's existence to the others - information he knows she has because she stole the report, he was even complaining about it. Also, the existence of Ikusaba could be kept a secret for a couple hours at best, because then the class trial starts and it becomes obvious that everyone is still alive, so the corpse has to be a third party. Finally, he outright tells Byakuya there's a 16th student, so he can't have wanted to keep Ikusaba's existence secret.
That means something on or about her face or body, which were covered up, is damaging to the killer(Monokuma, who covered her up and planted the bomb to destroy the rest of the evidence). He doesn't care if people know Ikusaba exists, but he does if people are able to view Ikusaba's exposed body.
I can think of two reasons.
1) Ikusaba's old wounds are a tipoff about something
2) Ikusaba's face is a tipoff about something
Try to picture it. Say the bomb doesn't go off, the students reach over and peel off the mask, the coat. What do they see? Well, presumably they see some random stranger's face, as none of them know Ikusaba, covered in unidebtifiabke wounds. This wouldn't be threatening to Monokuma at all.
My idea? I think that they
would
recognize the face behind the masks, and the source of the wounds. Because I think that
Mukuro Ikusaba was disguised as a student and fake-executed by Monokuma
. Here's why: it's clear to me that Ikusaba was almost certainly a Monokuma spy, in the same vein as Sakura. It also explains how Monokuma managed to get hold of stuff like machine guns for the changing room doors, and set them up, and why Ikusaba's existence was kept secret from the others. If that's the case, then she either adopted the role of an outside spy, watching from the shadows, or she infiltrated the group, like Sakura did. The latter theory makes more sense; Monokuma already has cameras, he needs someone to talk and prod people into murder from the inside; to act as a backup in case the notoriously honorable and wilful Ultimate Martial Artist went rogue. It would also explain why he doesn't want the students to see Ikusaba's face. And it also explains how Monokuma overpowered her - they were working on the same side, so she never saw it coming. It's possible that Monokuma told her she would be allowed to graduate if she worked with him, only for that hope to turn into despair, in classic Monokuma style, once she realized she'd been betrayed.
We know Ikusaba was hidden amongst the first fifteen, and we know she's not Aoi, Kyoko, Makoto(duh), Byakuya, Toko or Yasuhiro, because they were the ones investigating her death. Therefore it's clear that she was amongst those that "died", only to fake her death and slip away to join Monokuma until he betrayed her. We can rule out Sakura, Sayaka, Hifumi, Chihiro and Kiyotaka, because their bodies were thoroughly examined, and it would have been hard to fake any of their deaths. So Ikusaba set up a situation in which Monokuma would execute her; it would've been child's play to rig the executions, especially as the bodies of executed studenrs were not recovered afterwards.
Junko, Leon, Mondo and Celeste. Ikusaba must have been in those four. Given Chihiro, I won't deny the option of Ikusaba possibly disguising herself as a boy, especially since she'd probably be all muscular as a soldier. However, I'm extremely dubiois that she could fake being Mondo or Leon, given their hard to fake body shapes, deep voice and lack of chest(we know Ikusaba has visible breasts, Aoi comments on them). That narrows it down to Celeste and Junko, the obvious targets.
I think Ikusaba disguised herself as Celeste. As a fashionista, Junko would be too famous to impersonate, while a shadowy gambler whose face nobody has seen would be perfect. Furthermore, while it's true Junko's body was not examined, I'm uncertain how her execution could be faked, whereas for Celeste all Monokuma has to do is drop the truck and open a trapdoor underneath her at the last second, like a stage magician would. Then the wounds on Ikusaba's body would be the burn marks from the fire.
So the full story would be like this. Ikusaba was working with Monokuma, and infiltrated the students as Celeste. When the time came for her to fake her death, she executed an intentionally sloppy and over-elaborate murder plan, then let herself get caught(I refuse to believe for a hot second that a legendary gambler would break so easily under stress). The flames go up, the fire truck flies in, the trapdoor opens, and she falls into a secret room and joins Monokuma. After the fourth trial(Sakura), Monokuma hears Makoto's speech and gets worried they won't kill each other any more. He murders Ikusaba, who's unawares. This happened sometime before Kyoko stole the key, because that could never have happened with two people watching the monitors. He sets up the body like Makoto figured, and sits back to watch the fireworks, ready to frame and execute whoever gets voted up.
Am I correct? Wildly off tangent? Missed a key part of my analysis?