A very good question dear anon!
The plot of this game starts with Trials in Fear as Trials in 2 Darkness is actually both a prequel and a sequel at the same time.
In Trials in Fear, one rose was left by the end. Roses were needed for students to escape. This is what Mary would use to escape the world and begin trying to stop Monopuppet. Her brother Ryou was the host of Monopuppet during Trials in Fear and she wanted to save him, so using the power of the book she tried to go back and start the game she lost him in over again, ensuring to erase his memories as well as the others to keep Monopuppet away as long as possible as in the original game he gave up to him willingly much like in one of the later bad endings to Trials in Fear. Additionally this is also why trials in fear had a Mary post just before ti2d had started.
An additional thing to note is this is why prologue was executed at it's bizarre pace. The two book realities were begining to overlap and coexist with one another as new consumed the old. As a result things like Haruka's reflection acting differently to Haruka had occurred, it was the "first incarnation" appearing in the reflection instead of her current self.
Mary from the start of the game held influence in the book world but only so much as she only really managed pages. In order for her goal to be reached she needed another mastermind that was either the same the first round or someone new entirely, so long as they would not force Ryou into Monopuppet’s hands.Out of the book world, He discovered the book of the original game that Mary was repeating and once it clicked with He what was going on in game she sacrificed herself. He wanted to keep everyone alive whereas Mary was content with all of them dying again so long as she could save Ryou. He was not in full awareness as her monster puppet self Argos however, which is why she still initiated the killing game, but managed to keep some kids from dying through a punishment system instead of an execution one.
For Monopuppet, he was around since prologue and never left. There was always a clue of him directly in each chapter through art, event descriptions or both. Monopuppet in this ending basically got fed up waiting and pulled everyone into the dead space, which for the living is how it was described and endured in kind. Mary instead uses her last page to set the few survivors free and end the world with her still inside it because she knew she must attone for her sins. Her connections with the first mastermind also bound her to the book, making her erasure an important step in fixing the reality of the many lives she destroyed in her pursuits. This is the final ending.
Chapter 4 was planned to be the chapter Argos gains enough conscious to offer the actual exit to the game in exchange for one more life. This was where cellphones would be brought up as the special item of this game, as well as the game Monopuppet would intervine. After telling the class the truth about Mary Ryou was to give up his body again out of pure hatred for his sister’s actions and desire to escape the hell the book had created for them both. Chapter 5 was to be all about informing about the book and getting to know Monopuppet, chapter 6 was to be the end with mastermind trial and a final judgement call by the class for what she has done.
If fellow mods were involved enough in aiding the group running, there was also the bonus material of gag bad endings just like in Trials in Fear. Unfortunately due to circumstances both mods had dropped entirely during chapter 1 so this could not be achieved and this is the final result.
All of these set ups were pieces to an intricate story and were in their own rights clues to a much larger picture. However since half the game was scrapped in an instant a lot of it got rushed by the end so confusion is understandable.
Thank you for understanding.