Here's my massive headcanon, I guess.
At the beginning of the game, you would select whether you were a boy or a girl, ergo Persona 3 and Pokémon. If you said "boy", you would play as Ayushi Fujimori, and if you said "girl", which would be treated as the canon plotline, you would play as Ayumu Fujimori. The one you picked would be SHSL Bad Luck and the protagonist, while the one you didn't pick would be SHSL Good Luck, and a side character.
Case 1: The victim would be Ayushi Fujimori if you selected to play as Ayumu, and vice versa. They would have been stabbed in the nape of their neck and fall down a flight of stairs. The killer would be Kasumi Idumo, who would have had a psychic prediction of the SHSL Good Luck attempting murder and succeeding due to their luck, killing them in order to prevent it.
Case 2: The victim would be Nico Himuro, and she would have been killed by getting her head slammed into a table over and over again. The killer would be Maiko Kagura, who is "surprise!" actually a boy wearing women's clothing in order to honour his deceased sister. Nico would have been killed because she spoke ill of the dead, and Maiko would have none of it.
Case 3: The victim would be Garumi Ohsone, and she would have been killed by being kicked off a watchtower, dying on impact. The killer would be Souji Rokudou, and he would have killed because Monokuma's motive meant that his business would have been driven to bankruptcy if he didn't kill.
Case 4: The victim would have been Kazusaiyo Samejima, and he would have been killed by being blown to bits with a remote-activated cannon. The killer would be Kego Sakuma, and he would have killed Kazusaiyo due to not knowing what the remote control would do.
Case 5: The victim would be Mikoto Itsuki, and if you thought Komaeda had it bad, well, she would have much worse. She would have been bound and gagged with duct tape, stabbed with a knife, shot with a pistol several times and finally killed via being strangled with a piano wire. Her talent would be the SHSL Spy. The killer would be Hoshi Yodogawa, and as for why he committed the most sadistic murder of them all? Had Mikoto lived, she would have connected him to a string of murders outside of where the Killing Game took place.
Case 6: Surprise! Hoshi Yodogawa was just some psycho; the true mastermind behind Monokuma would be none other than Mizusu Aisaka. She had lured everyone to the location in order to sacrifice them in an effort to revive none other than Junko Enoshima. Luckily, she fails, she is executed, and the survivors are free to go.
The survivors would be Ayumu/Ayushi Fujimori, Koga Mitsunari, Akira Tsutaiya, Arushi Todoroki and Marin Mizuta.