Hotspots are areas that keep things in check inside of the simulation and they are easily visible because they are surrounded by a giant, red shield. In order to bring the shield down, you’ll have to find the generators (marked on your map as yellowish icons) and disable them. There’s usually two or three generators assigned to each Hotspot and you hold the designated button while standing in front of it to disable it.
Once you have disabled all of the generators, the shield will be brought down and you can go to the main controller. Of course, each Hotspot will be guarded by the Zin and while you don’t have to kill them all, it’s a good idea to do so to avoid getting interrupted. When the coast is clear, go up to the main console and hold the button to clear the Hotspot.