Turns out the bug that shut me down last time was less of a bug and more of a "me not seeing the manhole cover into the sewers, due to the pile of vaporized Enclave soldier ashes covering said hole".
Still, once I was in the sewer it was an easy matter for me to start sneaking around, vaporizing the Enclave soldiers that were in pursuit of our party. Laser rifles are wonderful things when you know how to use them and actually have one. :)
Good news is that eventually the Enclave soldiers stop bothering us. Bad news is that is because the escape tunnel is also being used by a couple of squatting feral ghouls and the Enclave soldiers were ripped to shreds despite their fancy armor and plasma weapons. Of course I am sneaky like ninja and manage to vaporize ghouls just as easily as I do Enclave soldiers.
The one hang-up? Doctor Li makes me stop moving about halfway down the tunnel. Seems that her head lab assistant has a heart condition and she doesn't have his medication. I briefly consider using my speechify skills to convince her to leave him behind but since she says she can treat him temporarily with a few Stims if I can spare them. Since I have about 60 of them even after being burned by plasma a few times, I agree and everyone is ready to go again in a minute.
There is another humorous moment where - after I find a few Brotherhood of Steel Paladins behind one door - I give the rest of my group the go-ahead to go on and a horde of zombies suddenly run out from the doorway I hadn't checked yet. The Paladins are on the case and shooting flamethrowers at the ghouls.... somehow not hitting the panicky scientists and technicians running between them and the sudden zombie invasion.
We come out the other side of the tunnel and it turns out that the emergency tunnel leads to The Citadel - the main fortress of the Brotherhood of Steel. Doctor Li shouts at their leader - a man named Lyons - over the intercom to let her in. Well, one thing leads to another, I am introduced to the boss-man and I am told to talk with him about what we need to continue my father's work.
Oh, and in the midst of this, I hit level 18 and gained another feat. I took Concentrated Fire, which allows me to do extra damage to any body part on an enemy for every successful attack I make. Hello extra-damage head-shots!