Looking for something quite similar but different to Lord of the Mysteries. MC that builds its reputation/power in different parts of the world by proxies. Secret organization/ not known to others outside the circle (do not recommend me secret whatever powerhouse / shadow powerhouse goddamnit) Gods/higher entities Wars, conflicts
This is an old one but why not Legendary Moonlight Sculptor? Yes, his world is an MMO, but as the story goes on his sculptures build his reputation, his actions change history and reshape the game world, and his power just grows and grows... I don't think there were secret organizations involved but hey, the worldbuilding and allies he picks up along the way are hecka fun to read.
Everyone Else is a Returnee The World Turned into a Game after I Woke Up Tensei Shitara Slime Datta Ken Basicly any overpowered mc in a fantasy world that is already completed would work for your request, but these are some of my favorites.
I have been recommended those novels many times guys. I can make a blanket out of the people that said that previously.
Throne of primordial blood takes a bit but does get there though definitely not as cool as Lord of Mysteries. It's also not very secret. I'm also just gonna be here waiting for more replies
The Death Mage Who Doesn’t Want a Fourth Time I never read 'Lord of Mysteries', but this matches pretty much everything mentioned.
This one half fits your request, half doesn't. Duke's Daughter who's Liable to Die and Seven Nobles. MC reincarnates into an Otome Game which had random elements to it. For example, while there's one game, there's over half a dozen different "mystery setting" scenarios that pop up randomly from the midgame, significantly diversifying the potential plot. The first major turning point of these scenario's (there's a few minor ones before then), is the person the MC reincarnated into, who had practically been introduced as the game's villianess before then, being killed and found floating down the river. So how does this fit your request? Well the MC's attempts to prevent or neutralize future threats to her life before it's threatened results in her accidentally building up both official and hidden connections that can manipulate the world either currently or in the future. This includes the capture targets, most of which are working diplomats despite being in magical high-school, and the game's MC roommate (not the game's MC, because that had some random elements as well, so the stories MC doesn't know who it is) as official, known connections. The secret connections would include spoilers, but I will say that while the MC doesn't have the power to move armies, she has created sufficient effects while hiding her identity that would change the course of wars threatened in the future.
Common Sense of a Duke’s Daughter Although it is not at the level of Lord of Mysteries it has MC that shapes commerce of the world.
Dungeon Defense Trash of the Count’s Family To Be a Power in the Shadows! I really recommend these three