The repartition between free access areas and restricted areas may seem arbitrary at first, as in the same building there are free rooms and restricted rooms (or sometimes a restricted square in a free room), but makes perfect sense when you think about it. Restricted areas include: roofs, places located behind banks / store counters, store backrooms, autopsy rooms in a morgue, motel rooms, offices... They are either places in which anybody spotted there becomes suspicious (roofs), places where civilians aren't forbidden but you shouldn't enter ((motel rooms, since the team aren't supposed to be customers), or "employee only" places.
A few features adding difficulty aren't here for the sole sake of adding challenge, but are actually subtle examples of Surprisingly Realistic Outcome:
Why does executing an agent costs so much money? Because you are killing them in your HQ, so you have to actually hide the corpse thoroughly and ensure it can't be traced back to your people. Whereas on field missions, agents will leave the area for good in a few minutes and thus can just dump bodies out of sight.
Why do you raise the danger meter if you have a "compromised evacuation" (i.e. you didn't hurry enough to leave the place once the evacuation vehicle arrived on site)? Because witnesses noticed suspicious people getting into a suspicious vehicle, which gives clues to Beholder Initiative about your action, and possibly pieces of information which can be used to help them locate your hideout.
Why does danger skyrockets if you bring captured agents to your hideout (once you research the interrogation room)? Because Beholder Initiative starts frantically looking for the hideout, probably to either free their agents before they talk or silent them to ensure they don't.
It's also likely that the captured agents are also trying to free themselves, or secretly feeding intel to the Beholder Initiative while in prison - they are trained agents, so they were likely trained on what happens if they get captured by an enemy agency...
Notably, the upgrade that keeps enemy agents from raising your danger level is "Faraday holding cages," keeping whatever secret transmission devices they have from working. So they are indeed trying to emit a distress signal of some sort.
During the campaign, at one point, the protagonists receive a package include a tape. After listening the tape (which sounds unintelligible to the Player Character), the behavior of their original handler (whether it's Fender, Cyclone, or Delilah) starts changing, and they eventually betray the Cabal. Further investigation discovers they have all been turned into ManchurianAgents during the Seventies, when they were all trapped in a Vietnam prison, and taken from there by The Men in Black to the MK-ULTRA blacksite in Yugoslavia. This tape was probably their Trigger Phrase.
Why are there mercenary soldiers in Soviet nations? Well, those PMCs probably have a vested stake in seeing the Komplex's plans come to fruition, meaning Beholder and Valhalla were able to bring them on board as well.
Leslie gets killed during the 1983 United States embassy bombing in Beirut, and the game strongly implies he was the target. He actually is killed during a phone conversation, while he was scheduling a rendezvous with Deadpan. If the suicide attack had happened later, the Player Character may have have been killed, too.
If you look up the names of the chemicals used in Body Engineering, most of them (that aren't made up) are illegal anabolic steroids. With plenty of nasty side effects. Yeah, congratulations on turning your agents into roid-heads, You Monster!
