Comedy + Family/Sect/Kingdom building Do not recommend To Be a Power in the Shadows. Looking for something similar to Lord of the Mysteries
Trash of the Count’s Family -He makes his own secret organization to counter the other secret organization.
Kill the Hero Ototsukai wa Shi to Odoru (the organization itself isn't a secret but they hide their identities and have hidden motives) Slow Prison Life
Maybe something like: Evil Organization Recruitment Ads Baito de Aku no Soshiki Shadow Hero’s Everyday Life Animes/mangas: Gundam 00 Full Metal Panic!
Legend of Ling Tian Akugyaku no Black Maria Running Away From The Hero! The Absolute Evil for My Hero