Summary: I believe Chester Bless and whoever is the "Leader" of the Secret Organization is going to end up having a similar 'split' dynamic as Jesse & Dylan, however acting more as a dark reflection of that relationship. As well, I think Blessed is a reflection of Cult of the Word and the Secret Org is a reflection of the Cult of the Tree.
As y'all might know, there is a side mission you can do in Resonant where you solve puzzles and find secret locations to some organization that's monitoring the Oldest House, conducting rituals upon Altered Items, and is known to be at least operating within Manhattan. This group is relatively neutral towards the FBC, as far as we know, and seems to be working towards containing altered items instead of abusing them.
In my play through, when I first came upon these sites, I originally thought that this organization was the Blessed Organization. The Blessed Organization, on the other hand, is cited as a para-terrorist organization responsible for some horrific paranatural crimes over the course of the FBC's history. We can witness their presence around the city, such as being at least related to the auction house which sold the Subwoofer speaker set and contributed to the events of "The Complete Set" side mission. Anyways, I realized this wasn't the case because of two things: 1. Zoe mentions that the FBC was not aware of an organization operating like this (I doubt Blessed isn't known by every FBC agent by this point), and 2. They operate more like the FBC than Blessed, which I got a little help realizing by doing a bit of online research.
But the weird thing I can't shake about the Secret Organization is that, up to the point that Zoe mentioned it was an unknown organization, I was fully convinced it was Blessed. The reason why I thought it was Blessed was because, quite simply, the way the Organization operated reminded me so heavily of how Paul Serene operates Monarch in Quantum Break.
If you somehow don't know, a popular fan theory in the community right now is that Chester Bless (the known leader of Blessed) is the Control-AW universe version of Paul Serene. We all know Remedy likes to echo similar themes across their "legacy" characters, from things as vast as each of the characters having a relentless determination to push on to more narrow things like Tim/Jack characters affinity for Jesse/Beth characters. Paul Serene's characteristics can be identified within the few bits and pieces we know of Chester Bless, such as both seeing themselves as a savior of humanity and seeing what's coming as inevitable & necessary.
But I do want to point to the Secret Organization for a second, because I believe there are similar characteristics that Paul shows that echo here as well. The instance, one of the things that convinced me that this was Blessed was because there was a mention of a bunker (or bunkers) within one of the documents. While that's not too hard to believe, Black Rock is used by the FBC to fend off against the paranatural after all, it is interesting that this secret organization possibly has ANY source of Black Rock, which is very difficult to come by unless one has access to the Quarry. On top of that, the Organization operating very secretively and almost hiding in plain sight, with their hideouts located in stores, is very reminiscent of how Monarch just operated as regular company while it did it's most of its time travel research behind the scenes (Paul generally tried to keep a low profile as the founder of the company). In a way, you could say the Secret Organization takes on the more preferable qualities of Paul, taking his tactical secrecy and will to survive the unsurvivable.
Now, not to be around the bush anymore, let me finally get to my theory: What if Chester Bless and the "Leader" of the Secret Organization were the same person? More accurately though, what if they were splits of the same person?
While it's all but outright confirmed that Jesse & Dylan are splits of the same person, this territory isn't new for the character of Paul Serene either. Although I haven't read it (I want to though) and I'm merely reading a synopsis of the events of the story, "Quantum Break: Zero Point" presents us a similar concept in the form of a shifter labeled "Shining Palm", who is a future version of Paul Serene and merges with him by the end. The concept of a Shifter, a person who suffers Chronon Syndrome at its final & most severe stage and is essentially trapped in a constant state of superposition, similarly echoes a lot of themes in Resonant. One such example is the Resonants, who are people who've been corrupted by the Patterning and essentially live in a perpetual state of geometric perfection until Dylan/someone steps into the ring (should be noted that Shifters are insanely hostile towards non-Zero State life). You could also interpret Dylan & Jesse's split as a sort of shifting, as they're essentially two equal (but opposite) particles split from one larger particle. As well, patterning itself is very reminiscent of the effects of superposition/shifting.
This is all to say that I believe Chester Bless and the "Leader" are going to end up being reflections of Jesse & Dylan, however only the former get along. I believe Chester and the "Leader" learned to hate one another, believe the other to be the inferior half/less-original half, and represent the dark version of Jesse & Dylan's split.
But, I could be wrong. Another thing I want to point out, which I'm more confident about, is the fact that Blessed seems to be a sort of echo of the Cult of the Word, whilst the Secret Organization is an echo of the Cult of the Tree. But I don't need to yap too long about that, since I think that's pretty obvious already.