"Finally, the New Class. The class Nagito and I basically have no control. We made their life hell really. That's why the Neo World Program was created really, it's because of us. We probably took it too far..
We forced them to join us really, or face the consequences. We made an example of that to Kayo Ishii, brutally and methodically killing her, slowly. Ahh that was a great time, seeing their faces look so despair, because it would've been them if they didn't follow us. Luckily, everyone followed and became a Remnant of Despair. For months, they were strategically hunted down and captured by the Future Foundation, every single one of them.
The Future Foundation went on to make the Neo World Program. Komaru was assigned to be one of the people who were going in to the program, as Komaru was their teacher anyway. Playing as Kayo, Komaru entered the game. The program seemed fine, and all of the captured Remnants was programmed in. Minari was also sent in the game to help on the program's rehabilitation, at least so they thought...
Monaca gave Minari a USB device that would send the Monokuma virus inside that game, yet Minari doesn't know about what is in the device. So by installing Minari to the game, in the form of Kyroki Keiseki, they are just installing the virus. With Minari's installment, everyone in the game was trapped. In a final hoorah, Minari poisoned Kokoro's tea before the installment, and Kokoro died amidst in fixing the glitch. Oops."