Development of Lighthouse has been slow-to-none over the last couple years. Part of that is just the muses turning their backs on me, the other and larger part is trying to write a game of Lighthouse's particular political nature in Current Year(s).
To whit, the question for the last two years has been "in this game's setting, why hasn't the government just killed everyone yet?"
I don't know if it will kick me out of my creative inertia, but I do have some answers to it.
1. They Already Have
The Ecumene was destroyed over forty years ago by concerted effort of the military, the police, and the intelligence apparatus. The leaders were gunned down by agents of the Alphabet Soup or fled to the Underworld. Members were jailed, relocated, forced to recant, or threatened back into secrecy. The months-long siege was so brutal, and the decades of crackdowns to follow similarly so, that the anomalous underground is effectively dead in both the public and governmental consciousness. The battle has already been fought, and decided so completely, that there is little expectation that another Ecumene might form. We have been rendered toothless, obsolete, scattered and disorganized. Organizations like Lighthouse are permitted to exist because they are not judged a threat.
2. The Agency Doesn't Have Unlimited Budget
Unlike our friends over at the SCP Foundation, the Agency does not have a magic box that prints money. A government black-budget might be practically equivalent to that, especially in a narrative sense, but they cannot deal with everything everywhere all at once. There are so many little paranormal instances occurring every day that it's impossible to investigate all of them. They need to prioritize. If it is not a threat, someone in an office can mark the file as "No Follow-up Needed" and get on with their coffee break. All the little things, it's just background radiation.
3. The Agency Is Not On Good Terms With Police
Self explanatory. There's no love lost between the two forces - the Agency considers the police a bunch of trigger-happy bootcamp washouts who parade their ignorance like a pride flag, the police consider the Agency to be a bunch of deep-state spooks with no knowledge of anything on the ground who come barreling into their turf only to make everything worse. Neither party is happy at being forced to cooperate, and will often do only the bare minimum in terms of an operation.
4. The Government Is Focused Elsewhere
Politicians get better results in the polls from attacking climate refugees, abortion rights, and trans folk. Those in the Know are still a useful target, but the days when they were the great enemy to rally against are long over; Paranaturalists have been bundled into the great manila folder of acceptable targets.
5. Those In The Know Have Gone To Ground
While everyone is more or less aware of the anomalous, those who are active within it have, by necessity, grown good at hiding their involvement. In the times when that's not enough, there's a greater ability-willingness-necessity for escaping to the Underworld - a solution filled with its own dangers and hardships, even if it's only a temporary stay. It's entirely possible, and common enough, that those who go into the Underworld are so changed by it that they can never return to the Surface. But that's a risk people are willing to take, as the Agency lacks a solid foothold in the Underworld (save the attempts of TOWER division), and the government has no presence at all.
6. The Unknown Unknowns
This point is hearsay and speculation, but it is thought by many In The Know that the Agency is tied up in something that's drawing resources away from The City and other hotspots of activity. There's no telling what it is, and the only evidence is the absence of Agency operations where it's believed that there should be, and folks are split on whether this is a good thing. For the time being, at least, it allows for some expanded ability to move and act on the Surface, so long as the boat isn't rocked.