I've read the most of the Wiki, saw all of the Sakura content, and played a good chunk of the game, so I could give a general outline of the story:
Main Characters
- Mr. Saikou - Current CEO of the worlds largest corporation, Saiko Corp/Inc?
- Megami Saikou - The final rival and the CEOs daughter.
- Ayano Aishi (Main character) - "YanChan", the batshit insane serial killer girl you play as.
- Headmaster - School administrator for something like 25/35 years (A long time)
- Kencho Saikou - Younger brother of Megami and oldest sibling. Son of Mr. Saikou
- Senpai (Taro Yamada) - The main dude that you are attempting to manipulate into being your husbando
- Ayano's Mother - Was in the school in the 1980s. Committed various murders and got her version of Senpai, giving birth to Ayano as a result.
Now here is where the story begins:
- Saikou Corporation exists because of a grudge that Megami's grandfather held against the rest of the world.
- This grudge stems from his extreme nationalism and witnessing firsthand the bombing of Japan by the US in WWII, and watching his friends die before him.
- This nationalism is so great that he voluntarily joined a drafting Japanese military to fight for his country, during a bloody and intense war.
- Angry at the world, he sets out to create the largest corporation and spread the Japanese way across the planet, in a "revenge" attempt against everyone who wronged his great nation.
- He manages to succeed at this, creating the largest company in the world, but realizes that his plan won't work because Japan is already loved by a majority of the planet for its cultural and entertainment significance, and spreading its influence isn't really possible at this point.
- He gives up on his plan for world domination and idles around for some time before handing the company off to his son, the character known as Mr. Saikou.
- But before this, the grandfather opens a school, the Academy, as a "CEO training ground" for his son and grandchildren, putting the Headmaster in charge (We don't know his significance yet)
- In the first few years, the 1980s, Ayano's mother enters the school and goes on a similar serial killing spree, causing the Headmaster to fall into a deep depression while his schools reputation tanks and no closure is met. The headmaster becomes fat, turns into a bathroom-filming pedophile, and created the tapes (Headmaster tapes) as a coping mechanism.
- Jumping to recent times, Megami is being trained by her father to be the next CEO of their company, and is being enrolled at the school. She, the Headmaster, and the current CEO know that Ayano is at the school, but by the order of the CEO, the Headmaster is not to intervene.
- It is because of this deal that nothing changes about the school when you murder students. The only actual changes are when you either kill enough students that the school legally cannot continue operating, or a student council member which pisses off Megami greatly and she ends up having cameras and metal-detectors installed in the school.
- The no-intervening deal is because of a strange relationship between the Headmaster and the CEO, and its also hinted that Ayano's mother is involved in this as well, somehow.
- No idea of the significance of Senpai (Taro) yet, but he is somehow related to all of this.
- It was said by Alex a few weeks ago that the lore goes back to the 1700s... Nothing on this yet.
- The student council has its own lore, but it isn't related to this, so I'll leave it out. Their significance is nothing more than students at the school that Megami was friends with/recruited.
There is a bit more that I'll include later, but this is the jist of it. Angry Japanese WWII veteran creates company to take over the world, but ultimately is defeated. He creates the school as a "CEO training ground" for his son and later grandchildren. Headmaster is appointed, and a bit later in time Ayano's mother comes into the school and murders people. This makes the headmaster depressed as his schools reputation falls, but she gets away with it, and in the case of Ayano herself, he can't do anything about it.
Also should mention that Alex describes Ayano as someone who feels empty without Senpai, but doesn't necessarily enjoy it. He states that she wishes that she could fix her "condition" and that murdering people is something that she doesn't like very much, but has to do for her own good.