SECRET SOCIETIES is a book containing many of the antagonistic organizations Nephilim may encounter. The book includes much useful information, such as secret organizations, rules for creating Homonculi, rules for activating Orichalka, the Secrets of the Solar-Ka awakening, and more!
Kenneth Hite (born September 15, 1965) is a writer and role-playing game designer. Author of Trail of Cthulhu and Night's Black Agents role-playing games, Hite has been announced as the lead designer of the upcoming 5th edition of Vampire: the Masquerade.
To be the ultimate antagonist book for Nephilim, this is a good start but in the end it would be twice or thrice its size if you added most of the common lore about them. Still, it is an amazing cadre of information with a lot of resources, and it leaves you with the homework of reading more.