Ok, here goes, some slight alternations of the sequence of events to make it easier to explain.
-Alice thinks her mother killed herself. SURPRISE! She was killed by the organization.
-Alice is told by the school nurse that she killed her mother. Alice defeats her and the nurse kills herself.
-Alice meets Hornet and SURPRISE! He's actually her father. He was approached by the boss years earlier to become "hornet" and had to go kill his family. He got poison from the nurse and killed his wife, but didn't kill Alice.
-"The organization" is world-wide and exist to stop over-population. They aim to kill half the population on the planet.
-The Army Ant Queen is able to enslave people by swapping bodily fluids. Once she does, she can control them and people become like super-strong zombies who fuck others to "infect" them. The idea is to let them loose and infect a ton of the population, causing an epidemic, which will eventually lead to them all dying off.
-SURPRISE! The Army Ant Queen is actually BIG TITTY GIRL, controlling everything behind the scenes. The SC president was a timid, meek girl who she had sex with and enslaved.
-BIG TITTY GIRL cons Alice into having sex with her by having the SC president say that she wants to humiliate both of them to let them live. This is a ploy to swap spit and infect Alice.
-BIG TITTY GIRL wants to humiliate and control Alice because...she's jealous?
Because after all the bullying and the shitty life, Alice remained
positive.-SURPRISE! Alice knew BIG TITTY GIRL was the real bad guy before teh sexxor and used her wire to create a trap. BIG TITTY GIRL DEAD.
-Without BIG TITTY GIRL's presence, all the "army ants" become mindless drones and just kind of stand around, although some get out of the school and start doing a zombie-like plague (only instead of killing and eating people, they're all fucking
)
-Alice goes to the roof of the school and meets her father and kills him after they fight. The end?
-BUT WAIT! Remember the girl who bullied Alice and then became friends with her? Alice thought she was killed by the nurse. Nope...she survived and in fact
SHE IS THE BOSS. 
(She did nothing all this time and just stood around looking helpless)
-BUT WAIT AGAIN! This girl isn't a normal human! She looks 15, but is actually 100 years old! (Of course!)
-The boss looked like a 10 year-old for most of her life (of course!) and found that she was able to manipulate people like a parasite bug controlling another insect. She found that she could only have total control over one person at a time, however, and these became her "hornets."
-The boss used her power to control powerful men and it is indicated that she is responsible for causing multiple wars. There's a fucked up scene of a Japanese imperial army general reporting to her as she sits in a chair that's way too big for her.
-At some point her immortality fades a bit and she ages to look like a teenager.
-AND OF COURSE she also wants to mess with Alice because...reasons...and has planned out everything that has happened up to this point.
-Alice gives no fucks and throws her off the roof. Boss = dead.
BUT WAIT YET AGAIN! The zombie-fuck army is still out there as are most of the organization. Alice goes into hiding with one of her suriving pals, codenamed "Cockroach," who is a shifty, sneaky schoolgirl who wants to get into Alice's pants. She tries to do that again but Alice has left their hiding spot.
Alice is then showing beating up zombies and...that's it. We then get an epilogue of two of the characters saying that Alice is disappeared and has probably been taken by the organization and they're gonna get her back and...that's it.
