BDC1-1b

After the party does some patrolling and/or preliminary research they should call Mac or he can call them and check in on their progress. He can then tell them he got some info from another source that confirms zombies and that they seem to be behaving in a herd like manner and that they should track them. He gives the party a tracker to follow the zombies back to their daylight resting place. The behavior of the zombies (i.e. not walking around during the day) is the first clue to the necromancer controlling them. The tracker leads to the sewer, it is filled with a few zombies at first and then more and more as they get closer to the source. The source being the entrance into Atlas labs, which earlier that day was zombified. Once they get to the top office and find the paperwork the alert goes out and Mac calls them telling them to GTFO as Atlas is going to firebomb it. Atlas labs also has a clue as to the Resistance (mainly that it exists and they are afraid of it).

They can flee back through the sewers or some other genus PC way. If they go back through the sewers they have a chance to notice the secret path that takes them to the church. This might be found earlier if they are really good at their searching, which can bypass the lab (they will still have to come back and clean it out once they realize Father Joseph is actually a former scientist there and has been selling them bums.) If they do skip the lab and go directly to the church they probably wont get the Resistance clue.

Atlas ends up trying to clean up the lab in the most efficient manner by blowing that shit up...its the only way to be sure.