Lincoln realized he seemed to have been reincarnated in a strange other world. The Abyssal disaster had wiped out 99.99% of the population. Men were almost extinct. With the organization's help, the surviving girls mastered the power of the Abyss to fight the disaster and rebuild their home. He was the one who founded the organization. He was also the source of the disaster. It was all for the sake of evolution.
"So I'm the final boss, right?"
Looking at the girls breaking down after learning the truth, and at this world left scarred by the Abyss, Lincoln felt that he had to do something.