TD: Heroine loses to Seiga, she turns the heroine into a zombie via Yoshkia bite. They become a mindless slave to the Taoists. And if it's Reimu, Miko fills the power vacuum by destroying the Hakurei Shrine and becomes dictator of The Human Village. Many heads are chopped off for being "youkai sympathizers".
PCB: With the Heroines out of the way, The Saigyou Ayakashi awakens! Yuyuko poofs out of existence, Youmu is confused as hell, and then DIES. Yukari wakes up and realizes it was a mistake to do a favor for Yuyuko while half-asleep. Then cries because she has lost her
love friend again, and it was her fault, she probably kills herself after this. Winter stays eternal, the crops die out, a cult known as "The Sisterhood of the Cherry Tree" springs up to try to calm the Saigyou Ayakashi by sacrificing black haired girls to it. Nothing works. All of the humans DIE cause no food. Then all of the Youkai DIE cause no food.
EOSD:
This fanfic happens.Can't think of any others.
EDIT: Wait, DDC: Sejia DEFEATS the Heroines. The Youkai rebellion continues, and all of the Human Village gets eaten (And before you ask "BUT WHAT ABOUT KENIE", Kenie was in her Youkai form at the time, so she also goes CRAZY with bloodlust). All of the Youkai DIE cause no food. Sejia gets bored because she won.