That is a difficult one.

First thing I would ask is "What Government agency?" I'm not in the US, so obviously cant really do a proper comparison, but if they were getting checked over by the tax department then that alters the priorities of things.

The next thing I would do is ask for some contact details so that I could contact the people in the offices for extra info if possible, at the same time it would probably be a good idea to find out what the political/emotional atmosphere is like. You dont want to walk in and start telling the newly aquired staff what to do, probably wouldn't go down too well.

Then comes the more formal stuff of finding out what these databases do, what interfaces use them, who has access, do they need access and so on.

To be honest, the audit of these systems (to me) comes last after you start building the bridges with the overworked staff, if they arent co-operative then you don't stand a chance of getting things sorted.

Probably many other things I could write for this, hell, this is an entire thesis case study, but I have work to do 🙂