Below there is a summary of selected extra activities in Downtown, specifically those, which may prove a bit problematic.
1) Mobile Command Center - There are three Jammers in Downtown district, although they are remote from the main base in this location. Each Jammer is, of course, located on a rooftop, and the easiest way is to destroy them is by attacking from a distance. But it is not really required, the more that they are defended rather poorly.
As for the base, getting close to the mobile command center will cause as many as two enemy helicopters to take off. Obviously, you should use the best powers available (those under R1) and stand in such places (e.g. on low roofs or covered balconies) so that at any given moment you were attacked only by one chopper. Shoot down the helicopters one after the other, and do not forget to refill heavy ammo reserves which is very useful to fall through with that plan. After securing the area well enough, get to the upper level of the central structure in the base, destroy the generators mounted in its side supports and then sabotage the main core.
2) Hidden Camera - The camera you seek is in the place shown in the above screenshot.
3) Audio Log - Once you start searching for the audio log, you need to examine the nearby square with a fish statue. The hard disc is lying on the ground, as shown in the screenshot.