Custom Command and Control Protocol
Adversaries may communicate using a custom command and control protocol instead of encapsulating commands/data in an existing Standard Application Layer Protocol. Implementations include mimicking well-known protocols or developing custom protocols (including raw sockets) on top of fundamental protocols provided by TCP/IP/another standard network stack.
Cobalt Strike allows adversaries to modify the way the "beacon" payload communicates. This is called "Malleable C2" in the Cobalt Strike manual and is intended to allow a penetration test team to mimic known APT C2 methods.
Duqu is capable of using its command and control protocol over port 443. However, Duqu is also capable of encapsulating its command protocol over standard application layer protocols. The Duqu command and control protocol implements many of the same features as TCP and is a reliable transport protocol.
If NETEAGLE does not detect a proxy configured on the infected machine, it will send beacons via UDP/6000. Also, after retrieving a C2 IP address and Port Number, NETEAGLE will initiate a TCP connection to this socket. The ensuing connection is a plaintext C2 channel in which commands are specified by DWORDs.
Properly configure firewalls and proxies to limit outgoing traffic to only necessary ports and through proper network gateway systems. Also ensure hosts are only provisioned to communicate over authorized interfaces.
Network intrusion detection and prevention systems that use network signatures to identify traffic for specific adversary malware can be used to mitigate activity at the network level. Signatures are often for unique indicators within protocols and may be based on the specific protocol used by a particular adversary or tool, and will likely be different across various malware families and versions. Adversaries will likely change tool C2 signatures over time or construct protocols in such a way as to avoid detection by common defensive tools. 
Analyze network traffic for ICMP messages or other protocols that contain abnormal data or are not normally seen within or exiting the network.
Analyze network data for uncommon data flows (e.g., a client sending significantly more data than it receives from a server). Processes utilizing the network that do not normally have network communication or have never been seen before are suspicious. Analyze packet contents to detect communications that do not follow the expected protocol behavior for the port that is being used. 
Monitor and investigate API calls to functions associated with enabling and/or utilizing alternative communication channels.
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