The main villain was Ikkyu, and like the rest of the Ijin, he was either an emulator or a (warped) clone of the
historical figure of the same name. His idea of trying to murder most of the world's population is meant to be because of his insane idea that he can then recreate society using just the societal elites (the Ijin) as a template for how the world should be. In other words, it was to then remake the world in his own image.
From what I understood, the book was necessary because it had Beethoven's DNA, which they used to create the Ijin of him, who would play the melody that carried the subliminal suicide message.
The villain's confusion seemed to stem from the fact that Yomiko was obsessed with regaining her book even though she had no idea that it was anything other than a book. He couldn't understand why she'd want back something that was, to her, just another book, since it had no real use that way. The irony at the end was that she fought so hard to recover her book, but then had to destroy it to create a parachute to save herself.
The Son Goku Ijin (the staff guy) was somehow able to use his Nyoi-bo (staff) to wound Nancy, though I'm not sure how. He does, however, get his hands on the book, tossing it to the insect Ijin, who flies away with it. However, that's all Son Goku is able to do, being too weakened to accomplish anything else. Ikkyu then kills him so he can't be taken prisoner and made to talk.