Adversaries may create multiple stages for command and control that are employed under different conditions or for certain functions. Use of multiple stages may obfuscate the command and control channel to make detection more difficult.
Remote access tools will call back to the first-stage command and control server for instructions. The first stage may have automated capabilities to collect basic host information, update tools, and upload additional files. A second remote access tool (RAT) could be uploaded at that point to redirect the host to the second-stage command and control server. The second stage will likely be more fully featured and allow the adversary to interact with the system through a reverse shell and additional RAT features.
The different stages will likely be hosted separately with no overlapping infrastructure. The loader may also have backup first-stage callbacks or Fallback Channels in case the original first-stage communication path is discovered and blocked.
An APT3 downloader first establishes a SOCKS5 connection to 192.157.198[.]103 using TCP port 1913; once the server response is verified, it then requests a connection to 192.184.60[.]229 on TCP port 81.
BACKSPACE attempts to avoid detection by checking a first stage command and control server to determine if it should connect to the second stage server, which performs "louder" interactions with the malware.
BLACKCOFFEE uses Microsoft’s TechNet Web portal to obtain an encoded tag containing the IP address of a command and control server and then communicates separately with that IP address for C2. If the C2 server is discovered or shut down, the threat actors can update the encoded IP address on TechNet to maintain control of the victims’ machines.
Command and control infrastructure used in a multi-stage channel may be blocked if known ahead of time. If unique signatures are present in the C2 traffic, they could also be used as the basis of identifying and blocking the channel. 
Host data that can relate unknown or suspicious process activity using a network connection is important to supplement any existing indicators of compromise based on malware command and control signatures and infrastructure. Relating subsequent actions that may result from Discovery of the system and network information or Lateral Movement to the originating process may also yield useful data.
- Moran, N., et al. (2014, November 21). Operation Double Tap. Retrieved January 14, 2016.
- FireEye Labs. (2015, April). APT30 AND THE MECHANICS OF A LONG-RUNNING CYBER ESPIONAGE OPERATION. Retrieved May 1, 2015.
- FireEye Labs/FireEye Threat Intelligence. (2015, May 14). Hiding in Plain Sight: FireEye and Microsoft Expose Obfuscation Tactic. Retrieved January 22, 2016.