What they're doing is generally not approved by the government, but they have enough influence to get away with such actions under the cover of military exercises or such. It's not like X-Com can go complain to the police, and if they go to the Council, the Council will point out that this is exactly why they pay you.
Sorry, but that doesn't really make much sense unless the military of every country the cultists are active in is also infiltrated at the highest level, not even considering what the general public would think about "military excercises" (utilizing foreign aircraft no less) regularely shooting down other (civilian? How are X-Coms craft identified to the public?) aircraft in their own country. MIB at least have some outlandish designs that can be "explained away" as UFOs. Do you know how much of a fuss a MIG-31 shooting down a helicopter near a major US (or European) population center would cause? This is something you'd expect to see during
an actual (civil) war.
To begin with, this would pretty much preclude any civilian air traffic. I'm not sure you actually realize
how much of an issue this would be. A countries military straight up would not stand for this, nor would any civilian security forces and the administration, as it would outright invalidate any authority the government has. A government openly yielding sovereignity over their airspace to a foreign power (which cults are at that point) is not something that would feasibly happen, given that even your bizarro world still has sovereign states and national power structures which are represented in the council.
From a storytelling and narrative perspective starting players out with this dimishes the impact later discoveries about other organizations have. How are the MiB really that much of a threat, given that cults can accomplish pretty much the same thing? Turns out
being a gopnik with a handgun is enough to bend entire countries (including their military and security aperatus) to your will. If they can do that, why don't they simply shut down X-COM? How did X-COM even get involved into any of this in the first place, given that even the lowly cults you fight in the beginning are
that powerful and can get
the government to explain away something that would essentially lead to civil war?
Correct me if I'm wrong, but the whole appeal behind X-COM, X-Files and the other mythology you've chosen to borrow from for the mod ist that they have some kind of connection to the real world. They are, on some level,
believable or
feasible. Something like this breaks suspension of disbelief on a very basic level (at least for me) because of the implications it has in-universe. Yes, there are other things that do that
to some extent as well, but they are not "MIG-31 shooting down my craft over the US" kind of obvious. If the entire civilian and military leadership of a country is on-board with that, and said military and government are also somehow part of the council, how does any of this make sense? How does the public accept this? How does the FAA/EASA/whatever equivalent accept this? Do they even exist? Is the entire world population outside of cults and shadowy organizations brainwashed to accept
everything? Does X-COM "unbrainwash" their engineers/scientists/soldiers prior to hiring?
It's just that this is a bit hard to make sense of, even given the other outlandish things encountered in tha game? Interdimensional battleships, evil aliens in flying saucers and stargates? Sure, we don't acutally have those. They can have any rules they want. Cults using cold-war era airplanes operating openly from their own airbases to shoot down other aircarft near major population centers and nobody bets an eye? Bit of a hard sell for me, given that this still takes place on earth, humanity is involved and involves real life countries.
