1. A first computer system comprising: one or more processing units; memory, coupled to at least one of the one or more processing units, wherein the memory stores an operating system, and wherein the operating system is executed by the one or more processing units; and one or more programs that run within the operating system, wherein a first program of the one or more programs is an agent that is executed by at least one of the one or more processing units, and wherein the agent includes instructions for: initiating a communication with a remote security system in order to obtain an authentication token that is uniquely associated with the agent; receiving a plurality of executable instructions from the remote security server according to a security policy assigned to the agent, wherein the instructions are received through an encrypted communication channel between the agent and the remote security system, and wherein the encrypted communication channel uses the authentication token; and executing, at the first computer system, the plurality of received executable instructions, thereby implementing a security policy of the assigned security policy, wherein the agent initiates all communication with the remote computer system, the remote computer system cannot initiate communication with the agent, and the remote computer system identifies the executable instructions for the agent by placing them in a command queue associated with the agent.