Command and control (C2) communications are hidden (but not necessarily encrypted) in an attempt to make the content more difficult to discover or decipher and to make the communication less conspicuous and hide commands from being seen. This encompasses many methods, such as adding junk data to protocol traffic, using steganography, commingling legitimate traffic with C2 communications traffic, or using a non-standard data encoding system, such as a modified Base64 encoding for the message body of an HTTP request.
APT28 added "junk data" to each encoded string, preventing trivial decoding without knowledge of the junk removal algorithm. Each implant was given a "junk length" value when created, tracked by the controller software to allow seamless communication but prevent analysis of the command protocol on the wire.
The Axiom group has used other forms of obfuscation, include commingling legitimate traffic with communications traffic so that network streams appear legitimate. Some malware that has been used by Axiom also uses steganography to hide communication in PNG image files.
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 obfuscation technique 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 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. 
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