I find the special "undercover" missions like beach and ski resorts to be some of the most entertaining scenarios in the game. More of these would be fun, both in variety and frequency.
I don't know much about the underlying mechanics of modding the game either, but given that proviso one idea that seems like it might be relatively simple
to make would be some undercover missions infiltrating theaters and entertainment venues. There could be several related sorts of adventures.
1) We get a tip something bad is going to happen at a movie theater. Investigating agents arrive to find that subliminal visual or audio in the movie has turned everyone in the audience into homocidal maniacs rampaging through the place. Or maybe it's something simpler, like a mutagenic chemical has been slipped into the popcorn that everyone ate, or bad guys dispersed some weird mutagenic fungus into the ventilation system.
2) We get a tip that a radio station is broadcasting hidden audio under their normal programming. These frequencies turn listeners into homocidal maniacs, into some kind of were-creatures, or maybe just there's reportedly a shockingly high incidence of suicide amongst listeners of the station. We investigate to shut the station down. Also, if you haven't seen the older movie "Pontypool," that would be good inspiration for storylines along this general direction.
3) We get a tip that a theater is staging a performance of a forbidden occult play, sort of like "The King in Yellow." Investigating agents find the actors are cultists, and the audience has either been driven insane or turned into some kind of monsters. Could be either occult or psi-related mechanisms involved.
4) Some kind of "phantom of the opera" is terrorizing theater-goers. Investigations reveal either that he is a cultist performing sacrifices, or some kind of were-creature, or some kind of psi-related fiend.
5) We get reports of a major disturbance at a dance hall or concert. Investigating agents arrive to find some strange frequency in the music has turned the audience members into some rioting monsters, or perhaps they've just been hypnotized in preparation for abduction for some nefarious experiment and must be rescued before some cult members load them onto buses.
6) We get reports that a movie director is planning to make an underground snuff film. It's a zombie movie-- using real zombies devouring unsuspecting actors! Agents need to infiltrate the movie set, arrest the director, save the actors, and eliminate the zombies. Maybe we also need to investigate just how the director acquired the zombies.
There could also be an undercover mission at a hostpital or clinic. Investigations reveal that patients check in, but they never check out. Maybe unsuspecting victims are being abducted for some kind of research, maybe they're being turned into
or who knows what else. This mission could unlock after discovering that the clinic was an advertiser on the radio station mentioned in #2 above, for example, or maybe the radio station is discovered after investigating the clinic and the fact it bought advertising time there.
These missions could all be in civilian clothes, with concealable equipment only.
Another thing that could be creepy would be if at some point in the game, a lower-level agent is randomly eliminated. We get a message telling us the unfortunate person committed suicide and was found in the barracks. It would have to be a random lower level person to avoid making the player rage-quit in case their favorite veteran got eliminated. Anyway, we find out the dead agent went insane after handling some occult artifact (again, maybe reading a "King in Yellow" script), or maybe they just couldn't handle the stress of comprehending aliens and eldritch beings. Some minor investigations (research and item acquisition) could be required to prevent this from happening again, or else occasionally another agent is found dead in the barracks.
Maybe these ideas aren't practical, or range too far outside the themes you want to explore, or there just isn't time to work on them. On the other hand I haven't actually finished a playthrough yet. The mod is already very good, and already filled with loads of content for players to explore
, so for all I know you already have something like these things in there somewhere. Anyway, keep up the good work.