So at the start of presumably your second day of school (already starting in an entirely new school due to the incident yesterday), you come across with new students, new staff members, all of the old students, and even the old janitor and Ms. Applegate.
After doing those, you either end up helping Nugget with his new Nugget Cave, help Buggs get his knife back from Penny and kill her, and/or help Felix kill Teddy.
When those are done, you end up making pills for Ms. Applegate which she's gone mad crazy for, and you help Jerome defuse his "Billy" bomb.
After that, you go to the final mission where you kill off the teachers, get Bob to fend off a monster in the sewers, and save the 3 kidnapped students.
If you bother to get all 50 monstermon cards, you watch everyone but you, Nugget, and presumably Billy, die from either being struck by lightning or turned to dust.