Unofficial Fallout 4 Patch

I had a close look at this navmesh. I started with the entrance hall and navigated along the path taken during the quest, all the way through to the end. Then I did this again to make sure that I hadn't left out any navmesh sections in rooms aside from the main path. I did not find any issues. This is in fact the best navmesh I have seen in FO4 so far. There's only one minor flaw in that a ledge on the upper floors is missing a drop down marker, so your followers can't jump down when you do and have to take a lenghty detour.

The gunners in the locked rooms could get out fine if they tried to, because there's nothing blocking their paths. But they don't try, because they have packages running that keep them within triigger boxes centered on the individual cells. The intent is obvious, once you make your way into the control room on the upper floor: they have been put in the roles of test persons and you can watch them deal with the traps which you can set off by pushing the respective buttons. This would be missed entirely when they would run off (and attack you) after picking the door locks, because you cannot get to the control room without passing through the section with the test rooms first. Of course, it will still be missed if you are the kind of person to shoot everyone on sight, but then you're probably a helpless case anyway.

Any problems you may have encountered are thus likely the result of a poor follower AI (which has however been improved by Bethesda in an official update AFAIR).

I added the missing drop down marker.