[spoilers for Protectorate questline]
Hi - first off I realize this could also be placed in the bug report section so excuse me if you think it should be there.
When one gets to the final mission for the protectorate and is ordered to gas the drones it's possible to instead go up the ladder to the left of the pipe where one would insert the gas and just kill them all. It's a relatively tough fight and I thought a really nice (and tough) way to get around the (frankly) stupid idea of turning your enemy into shambling monsters to wander the rails continuing to cause problems.
Unfortunately after killing them all the game totally fails to register this and you have to release the gas to progress all the same. I presume (but cannot yet confirm) that mutated drones will still show up as random events - even though this makes exactly 0 sense after they were all shot by glorious low AP burst attacks.
The easy (relatively easy anyway) fix for this would be to have the captain standing next to you as you release the gas and then give you a key to the ladder after you release it and it goes wrong.
The much harder fix (that I prefer but realize takes more dev time on an old game) would be to have this as a valid way for the questline to end. You choose to kill all the drones by hand - the gas squad are pissed but the local protectorate leadership rewards you (since they don't like the gas idea) and you get to be a part of making the protectorate a nicer entity. This would tie nicely into the persuasion ending to the renegade troops quest imo.
Anyway that's the issue and my suggestion - in replying if you please contain spoilers to this questline I would appreciate it greatly - I haven't finished this fantastic game yet!
PS: this twist in the protectorate questline felt cheap to me. The protectorate easily has the manpower and firepower to just kill them (hell just I do). This would be more efficient + believable but less able to push the the idea that the choice between anarchy and order is a tough one I guess
