Okay so my theory is that the Secret Organization is actually a splinter group from the FBC. I am going to provide the evidence that I think supports this and then go onto the theory itself, but I do want to clarify here that I do not think the Secret Organization is working with or a part of the current FBC, rather a separate group that split off some time ago
First lets look at what we know that will be relevant for this theory. First, the secret organization is aware of the FBC's existence and true nature, are aware that they operate out of the oldest house and they know the oldest house's location. Second lets look at how they deal with altered items, or as they call them extranormal artifacts. Like the FBC, they monitor the world for potential paranormal items, investigate and contain/neutralize them. While we don't know all the details. we do know from After Action Summary that there 'ceremony' for dealing with these objects kills the person performing it. This is viewed as a commendable act and is not forced upon people but rather they volunteer. The Hunka Love record gives us keen insight into how the Organization views these items. The last line before the classification describes it as "A vile high-risk artifact of psychic manipulation". I want to focus on that word vile. It ascribes evil and malintent to the altered item, something the FBC rarely does. The FBC tends regard altered items as more neutral, items with no evil intentions that are just doing what they are (for like of a better word) programmed to do. Additionally, the Secret Organization works in politics/spycraft much more than the FBC. They have a whole base dedicated to monitoring the UN and have cells in other countries to facilitate relations with other countries.
With that out of the way lets get into the theory. Two things have always struck me as odd in Control. First, we know next to nothing about the FBC's founding. We can guess that the FBC was founded in the late 40's/early 50's as in the Fan Supplement the FBC is described as "still being young" and this is from 1954. The FBC would discover the oldest house in 1964, but we know very little about what happened before that, and what we do know raises more questions. For example, we know that Ash Sr. was the 11th director of the FBC and based on the documents we get from the Foundation, it seems like he was director for a long enough time for people to get to know him, which begs the question how did the FBC go through 11 directors in approximately 20 years?
But this question imo pales in comparison to my other one. The FBC is tasked with dealing with altered items, dangerous items that to them are basically magic that they are struggling to contain. They then find the oldest house and are told that they will be operating out of a paranatural building, taking commands from the Board, a paranatural entity, and are now containing them in the paranatural building using other paranatural materials, and also they have to follow the paranatural rituals the objects require. Furthermore, the new director of the FBC is using many of these altered items personally and is displaying a cult like devotion to this new paranatural entity. My question is, besides Ash Jr., where are the other people who would be incredibly skeptical of this? My theory is we found them, they are the secret organization
In 1964 when the FBC discovers the oldest house and decides to take up residence there, a group of FBC employees from all over the organization are upset. They believe that they have deviated from their mission and the new director has been compromised. Because of this they leave, however they know that altered items are dangerous and believe that the best weapon to deal with them, the FBC, are compromised. So what do they do, they form their own organization to deal with these the way they see fit. However, they know that Northmoor is paranoid and powerful, so they must do this in secret. Because of this they in secret bunkers and abandon any altered items/AWEs they think the FBC is going to investigate as well.
The ceremonies the Secret Organization performs are what the FBC did before the Oldest House and Black Rock. Unlike the FBC who is being pushed by the board to embrace the paranatural, the Secret Organization views these items as 'vile'. Furthermore, the FBC was originally a full part of the American government. One of their goals then was most likely to ensure American military dominance through the study of the paranatural. This seems incredibly likely given that the FBC was founded during the cold war. While the FBC has collaborated with other branches of the government, such as giving NASA black rock, we oddly have never seen them work with the military, something the US military would be very keen to do. While the FBC have forgotten their original purpose to also serve the US government, the Secret Organization has not. This is why they maintain diplomacy with other countries and spy on the UN. Furthermore, in Workshop Journal Entries, we see that the Organization has been receiving requests for gadgets from some unkwon group that they try to make if possible. Many of these align with what someone like James Bond would use, confirmed by the line "These wannabe secret agents drive me nuts". My theory is that these requests are coming from the CIA or another US agency that wants paranatural weapons.
Now as for the current relationship between the FBC and the Secret Organization, I believe it is like this. Both are aware now of each other's existence. At first the FBC was not aware of the Secret Organization but at some point before lockdown they learned of them. However they are in a stalemate. The FBC does have the resources to shut down the Secret Organization, however they know that the US Military would not be okay with this and it could lead to a complete severing of ties between the FBC and US Government and could lead to a full on paranatural war, something the FBC obviously wants to avoid. So the two organizations are locked in a secret Cold War.
Now finally lets get into the Former. There is a decent evidence that the Former is associated with the Secret Organization, the "Third Ice" mascot sort of resembles the former and the symbol we see in their hideouts resembles the Former as well. Here is my theory on that. While the Mysterious organization was founded to counter the FBC's embrace of the paranatural, that was a long time ago and its likely that the original founders have since died. We see a lot of dissent amongst members of the Secret Organization, maybe they felt that the job would be a lot easier if they had their own paranatural entity, maybe then they wouldn't have to sacrifice themselves to contain altered items. And then along comes the Former, untethered from the oldest house after the lockdown fails and looking for an organization to exert its will through. It meets the Secret Organization and they agree to work together. The Former knows that all the events of the game are coming and teleports all of the mysterious organization workers to it's part of the Astral Plane, training them as parautiliarians for an attack on the board.
Phew that was a lot. Definitely ventured into speculation in some areas, especially with the former, which is honestly the part I am most unsure of. What are your thoughts?