When a human wears an interface chip, Emily can see through their eyes and move around the actual world with them. When she is not directly interacting with a human, Emily lives in a simulation of the world that runs on her servers. She has a dorm room that is a replica of a real grad student's dorm room, and she has built a simulation of most of the MIT campus and some of the surrounding city using live data from surveillance cameras and webcams, and still images of places where there are no cameras. The cameras have a 15 second lag so she experiences everything 15 seconds after it actually happens, which can be very frustrating when important things happen.
In this scene, people dressed like soldiers have stormed into the lab where Emily's team works, and Emily rushes in to see what is happening. However, she is not on interface with a human (until later, when Nathan briefly connects with her just before he dies), so is limited to the 15 second delay of her simulation and cannot interact with anybody.